title: Apln+ EC Rep1

description:
whole bone GFP+ cells
Apln_DP_fpkms.txt
Apln_EC-1

value: 8-12 weeks


title: Bone EC_DTX Rep3

status: Public on Nov 14 2019

type: SRA

city: Muenster

first: Hyun-Woo

last: Jeong

state: NRW

department: Dept. Tissue Morphogenesis

country: Germany

institute: Max-Planck-Institute for Molecular Biomedicine

description:
whole bone GFP+ cells
Vav1_fpkms.txt
Vav1-Cre-3

library_source: transcriptomic

data_processing:
illumina bcl2fastq (v2.19.1.403) used for basecalling and demultiplexing
Tophat (v2.1.1) used for alignment
HTSeq-count (v0.6.1) used for transcriptome abundance measurement
DESeq2(v1.18.1) used for differential gene expression analyses
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

molecule: total RNA

organism: Mus musculus

source_name: Femur/Tibia

extract_protocol:
Adult mouse bone samples were crashed with pestle, treated with collagenase IV, and digested to single cells. These single cell suspension were stained for FACS sorting. FACS sorted cell population were directly lysis into RLT buffer and RNA were extracted using RNeasy plus Micro Kit (Qiagen)
Double strand cDNA was synthesized using SMART-Seq v4 Ultra Low Input RNA kit for Sequencing (Takara) and sequencing library was constructed with Nextera XT DNA Library preparation kit (illumina). TruSeq Stranded Total RNA kit (Illumina) was used for the library preparation of total BMC and Lin- samples.

tag: strain

tag: treatment

value: diphtheria toxin

tag: age

tag: genotype

value: Vav1-Cre R26-DTR Cdh5-mTnG


title: KOV6: Long-term survivor (HG-U133A)

type: RNA

city: Brescia

first: Antonella

last: Ravaggi

state: Brescia

address: Viale Europa 11

department: Department of Clinical and Experimental Sciences

country: Italy

institute: University of Brescia

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45 °C on GeneChip® Human Genome U133A oligonucleotide microarray chips (Affymetrix, Inc., Santa Clara, CA, USA) following the manufacturer’s protocols. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner  3000 7G.

data_processing: The data were analyzed with Affymetrix Gene Chip Command Console Software, using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

organism: Homo sapiens

source_name: ovarian cancer

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA

extract_protocol: Total RNA was extracted and purified from snap-frozen biopsies containing at least 70% of tumor epithelial cells by TRIzolⓇ Reagent (ThermoFisher) according to manufacturer’s instructions.

tag: tissue

value: ovary

tag: tumor stage

value: IC

tag: tumor histotype

value: high grade serous

tag: phenotype

value: platinum sensitive


title: Bone EC_DTX Rep2

description:
whole bone GFP+ cells
Vav1_fpkms.txt
Vav1-Cre-2


title: KOV33: Short-term Survivor (HG-U133A)

value: omental metastasis

value: IIIC

value: platinum partially sensitive


title: KOV35: Short-term Survivor (HG-U133A)

value: platinum resistant


title: ND047

city: San Francisco

first: Ling

last: Bai

state: CA

address: 1550 4th St., Rock Hall Rm 346

department: Physiology

country: USA

institute: UCSF

description:
NGT_all_R1_RPKM_nocap_sg.csv
Vagal_TargetSeq

data_processing:
all samples: HighSeq 4000 were used for sequecing and de-multiplexed to generate a fastq file.
For Sample 1: De-multiplexing alignment to the mm10 transcriptome and unique molecular identifier (UMI)-collapsing were performed using Cell Ranger version 2.0.1, available from 10x Genomics with default parameters.
For all other samples: Reads were aligned to annotated mRNAs in the mouse genome (UCSC, Mus musculus assembly mm10) and the read count for each gene was calculated using ArrayStar software (DNAstar).
Genome_build: mm10
Supplementary_files_format_and_content: mtx file generated by Cell Ranger v2.0.1, including all cells in Sample 1
Supplementary_files_format_and_content: csv file include reads values for all cells (ND1-501) other than sample 1

source_name: Nodose ganglion cells

extract_protocol:
Nodose ganglion cells are dissociated using a combination of papain/collagenase/dispase solution. 10x Genomics (Sample 1) or Smart-Seq 2 (all other samples) was used to prepare cDNA library
Sequencing library is prepared follow the instruction of 10x Genomics (Sample 1) or using Nextera DNA Library Prep Kit (all other samples)

value: nodose ganglion

value: post natal 8-12 weeks

value: wild type


title: KOV4: Long-term survivor (HG-U133A)

value: IIB


title: KOV31: Short-term Survivor (HG-U133A)


title: Apln+ EC Rep2

description:
whole bone GFP+ cells
Apln_DP_fpkms.txt
Apln_EC-2

value: tamoxifen

value: Apln-CreERT2 R26-mTmG


title: KOV36: Short-term Survivor (HG-U133A)


title: KOV10: Long-term survivor (HG-U133A)


title: ND051


title: KOV44: Short-term Survivor (HG-U133A)


title: Bone EC_ctrl Rep3

description:
whole bone GFP+ cells
Vav1_fpkms.txt
Vav1-Cont-3

value: 8-12 weeks


title: KOV39: Short-term Survivor (HG-U133A)


title: Bone EC_ctrl Rep2

description:
whole bone GFP+ cells
Vav1_fpkms.txt
Vav1-Cont-2

value: diphtheria toxin


title: ND049


title: KOV50: Short-term Survivor (HG-U133A)


title: KOV47: Short-term Survivor (HG-U133A)


title: Bone EC_DTX Rep1

description:
whole bone GFP+ cells
Vav1_fpkms.txt
Vav1-Cre-1

value: Vav1-Cre R26-DTR Cdh5-mTnG


title: ND046


title: ND044


title: ND043


title: KOV51: Short-term Survivor (HG-U133A)

value: ovary


title: ND045


title: Bone EC_ctrl Rep1

description:
whole bone GFP+ cells
Vav1_fpkms.txt
Vav1-Cont-1


title: ND042


title: KOV38: Short-term Survivor (HG-U133A)


title: KOV37: Short-term Survivor (HG-U133A)

value: IV


title: KOV42: Short-term Survivor (HG-U133A)

value: high grade serous


title: GFAT-1 G451E rep#1

city: Cologne

first: Martin

last: Denzel

address: Joseph-Stelzmann-Str. 9b

institute: Max Planck Institute for Biology of Ageing

data_processing:
Fastq reads were trimmed using flexbar version 2.5 (-a ${adapters_file}  -ao 10 -u 5 -q 20 -m 20 -f i1.8 -ae ANY)
Fastq reads were mapped using hisat version 0.1.6-beta
Aligned reads were further processed using samtools
StringTie version 1.0.4 was used to identify transcripts
Cufflinks version v2.2.1 was used to merge, quantify and calculate differential expression of transcripts
Genome_build: GRCm38.dna.primary_assembly
Supplementary_files_format_and_content: Tab-separated values

source_name: neuroblastoma cells - N2a

growth_protocol: N2a cells were cultivated in DMEM (Gibco, 1 g/l Glucose) supplemented with 10%FBS and Penicillin/Streptomycin.

extract_protocol:
Total RNA was extracted using Qiazol reagent and the Qiagen RNAeasy RNA extraction kit according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols based on polyA enriched RNA samples

treatment_protocol: The 'treatment' set was treated with 10 mM N-Acetyl-D-Glucosamine (Sigma A8625) for 24h prior to sample collection. The treatment was supplemented to the medium.

value: carry a CRISPR engineered homozygous G451E substitution in GFAT-1


title: GFAT-1 G451E rep#2


title: GFAT-1 G451E rep#3


title: IA 4

city: Pittsburgh

first: Zixuan

last: Lin

state: PA

address: 450 Technology Dr

department: Department of Orthopaedic Surgery

institute: University of Pittsburgh

description: OC with IL-1β tratment, and celecoxib treatment on chondral side, modeling intra-articular administration of celecoxib

data_processing: Relative gene expression was calculated using the ΔΔCt method, with gene expression levels normalized to that of the housekeeping gene ribosomal protein L13A (RPL13A)

label: SYBR

source_name: iMPCs

label_protocol: Reverse transcription was performed using SuperScript™IV VILO™Master Mix (Invitrogen). RT-PCR was performed on an Applied Biosystems RT-PCR system using SYBR Green Reaction Mix (Applied Biosystems).

extract_protocol: Samples were lysed in Qiazol Reagent (QIAGEN), and RNA was isolated using the RNeasy Plus Universal Mini Kit (QIAGEN).

tag: cell type

value: iPSCs-derived MSCs


title: IA 5


title: KOV55: Short-term Survivor (HG-U133A)

value: omental metastasis

value: IIIC


title: KOV53: Short-term Survivor (HG-U133A)

value: platinum resistant


title: IA 3


title: KOV45: Short-term Survivor (HG-U133A)


title: KOV104: Short-term Survivor (HG-U133A)

value: not available


title: KOV52: Short-term Survivor (HG-U133A)


title: WT GlcNAc rep#1

value: WT

value: 10 mM GlcNAc, 24h


title: WT rep#3


title: WT GlcNAc rep#3


title: ND041

value: nodose ganglion

value: post natal 8-12 weeks

value: wild type


title: WT GlcNAc rep#2


title: ND040


title: KOV105: Short-term Survivor (HG-U133A)


title: SY 5

description: OC with IL-1β tratment, and celecoxib treatment on both sides, modeling systematic administration of celecoxib


title: IA 2


title: b-gal- F4/80high cells, replicate 1

city: Tartu

first: Mariliis

last: Klaas

address: Riia 23

department: Institute of Molecular and Cell Biology

country: Estonia

institute: University of Tartu

description: CCGY3ANXX_FITCneg1_18s003329-1-1_Jaks_lane818s003329

data_processing:
Illumina Casava1.7 software used for basecalling
HT-seq python package (version, 0.5.3p9, with flags–mode= union–stranded= no–type= exon) was used to count the number of reads aligned to the reference genes (genome build GRCm38.p4, Ensembl).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10(Mouse)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: b-gal- F4/80high cells

extract_protocol:
Cells from livers of Lgr5-LacZ mice were prepared for fluorescence activated cell sorting as described by following protocol. Briefly, under anesthesia the mouse liver was perfused via portal vein with pre-warmed (37°C) EGTA Krebs-Ringer buffer solution at 4 ml/min for 5 min, followed by perfusion with pre-warmed (37°C) collagenase type II solution (0.45 mg/ml, Gibco) for 15 min. Next, the liver was excised, cells were dissociated in Williams E medium (Gibco) supplemented with 5% FBS (Corning) by vigorous shaking and pipetting. The remaining undissociated liver tissue was further incubated in Pronase solution (0.5 mg/ml, Roche) for 5 min at 37°C. The acquired cell suspension was filtered through 70 um strainer and combined with cells from the previous step. Hepatocytes were pelleted by repeated centrifugation at 50xg for 1 min and collected for further analysis. Supernatant was further centrifuged at 300xg for 10 minutes and the pellet containing non-hepatocyte cells was incubated in red blood cell lysis buffer (BD Pharm Lysing Buffer) for 10 min on ice. The cells were then centrifuged at 300xg for 10 min and proceeded with FDG treatment as described in Kasper et al., Methods Mol Biol. Subsequently, the samples were centrifuged at 300xg for 5 min and the cell pellet was incubated in 1% BSA for 30 min. Next, the cells were incubated with fluorochrome-conjugated antibodies to EpCAM or F4/80 in the dark for 45 min. Nuclei were stained with 2.5 µg/ml DAPI solution for 2 min and cells were analyzed on FACSAria II flow cytometer (BD Biosciences). RNA from FACS-separated cell populations was extracted with PicoPure RNA Isolation Kit (Arcturus) according to manufacturer´s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

value: mixed C57BL/6 and CBA

value: 10-12 weeks

tag: genotype/variaton

value: Lgr5-LacZ transgenic

value: liver

value: b-gal- F4/80high cells


title: WT rep#2


title: ND039


title: ND032


title: Hepatocytes, replicate 1

description: CCGY3ANXX_HEP1_18s003333-1-1_Jaks_lane818s003333

source_name: Hepatocytes

value: Hepatocytes


title: WT rep#1


title: b-gal+ F4/80high cells, replicate 2

description: CCGY3ANXX_FITCpos2_18s003328-1-1_Jaks_lane818s003328

source_name: b-gal+ F4/80high cells

value: b-gal+ F4/80high cells


title: Hepatocytes, replicate 2

description: CCGY3ANXX_HEP2_18s003334-1-1_Jaks_lane818s003334


title: ND037


title: IA 1

value: iPSCs-derived MSCs


title: ND036


title: SY 4


title: b-gal+ F4/80high cells, replicate 1

description: CCGY3ANXX_FITCpos1_18s003327-1-1_Jaks_lane818s003327


title: b-gal- F4/80high cells, replicate 2

description: CCGY3ANXX_FITCneg2_18s003330-1-1_Jaks_lane818s003330


title: ND030


title: SY 3


title: ND035


title: EpCAM-positive cells, replicate 2

description: CCGY3ANXX_EpCam2_18s003332-1-1_Jaks_lane818s003332

source_name: EpCAM-positive cells

value: EpCAM-positive cells


title: EpCAM-positive cells, replicate 1

description: CCGY3ANXX_EpCam1_18s003331-1-1_Jaks_lane818s003331


title: SY 2


title: ND034


title: OA 3

description: OC with IL-1β tratment only


title: SY 1


title: ND031


title: OA 5

description: OC with IL-1β tratment only


title: OA 2

description: OC with IL-1β tratment only


title: CL 5

description: OC with no treatment


title: OA 4

description: OC with IL-1β tratment only


title: ND028


title: ND027


title: OA 1

description: OC with IL-1β tratment only


title: ND026


title: ND024


title: CL 4

description: OC with no treatment


title: CL 3

description: OC with no treatment


title: ND025


title: CL 1

description: OC with no treatment


title: ND023


title: ND022


title: ND020


title: CH OA 8

description: osteoarthritic CH tissue


title: CL 2

description: OC with no treatment


title: ND021


title: CH OA 7

description: osteoarthritic CH tissue


title: G800 DNAm

type: genomic

city: Toronto

first: Paul

last: Guilhamon

state: ON

address: 686 Bay Street

country: Canada

institute: SickKids

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using standard recommended Illumina scanner settings

data_processing: R package ChAMP v2.9.9

label: Cy5 and Cy3

molecule: genomic DNA

source_name: tumour sample

label_protocol: Standard Illumina Protocol

extract_protocol: Standard Illumina Protocol

value: glioblastoma stem cells


title: G797 DNAm


title: G719 DNAm


title: CH OA 6

description: osteoarthritic CH tissue


title: G729 DNAm


title: G744 DNAm


title: G613 DNAm


title: ND019


title: ND016


title: G706 DNAm


title: G705 DNAm


title: ND014


title: G648 DNAm


title: G702 DNAm


title: cox4d _t_58

first: Jason

middle: V

last: Rogers

address: 1170 Veterans Boulevard

institute: Calico Life Sciences LLC

data_processing:
Reads were demultiplexed using bcl2fastq2 v2.20.0.422
TPMs were calculated using salmon v0.9.1 and options --noEffectiveLengthCorrection
Genome_build: sacCer3
Supplementary_files_format_and_content: tab-delimited text file with raw, absolute TPM levels per gene

organism: Saccharomyces cerevisiae S288C

source_name: Saccharomyces cerevisiae

growth_protocol: 30 C ,200 RPM in YNB + NH4 + 2% glucose, 50 ml in 500 ml baffled shake  flask

extract_protocol:
total RNA was extracted using a standard yeast RNA extraction protocol (using hot, acidic phenol); briefly, cells are resuspended in a lysis buffer and acidic phenol, then incubated at 65C for 30 minutes to dissolve the proteins/membranes and release the RNA.  Next RNA is purified using alcohol precipitation.
RNA-seq libraries were prepared using purified RNA isolated as described above. RNA quality and concentration were assayed using a Fragment Analyzer instrument. RNA-seq libraries were prepared using the TruSeq Stranded Total RNA kit paired with the Ribo-Zero rRNA removal kit (Illumina, San Diego, CA). Libraries were sequenced on an Illumina HiSeq 4000 instrument.

treatment_protocol: Samples were collected for RNA extraction by vacuum filtration onto nylon filters. Filters were immediately placed into 2 ml snap cap tubes, submerged into liquid nitrogen and stored at -80°C until RNA extraction

tag: time, hours


title: U87-MG Replicate 2

city: Taipei

first: Ku-Chung

last: Chen

state: TAIWAN

address: No. 250, Wu-Hsing Street, Xinyi District

department: Department of Biochemistry and Molecular Cell Biology

country: Taiwan

institute: Taipei Medical University

description: miRNAs from  U87-MG

hyb_protocol: Fluorescent targets were hybridized to the Mouse Whole Genome OneArray® with Phalanx hybridization buffer using Phalanx Hybridization System. After 16 hrs hybridization at 50 C, non-speciﬁc binding targets were washed away by three different washing steps (Wash I 42 C 5 mins；Wash II 42 C, 5 mins, 25 C 5 mins; Wash III rinse 20 times)

scan_protocol: The arrays were scanned by GenePix 4200A 01 Autoloader (635nm power 100 PMT 320 ; 532nm power 10, PMT 335) and quantify the fluoresence intensity.

data_processing: The signal intensity of each spot was loaded into Rosetta Resolver System® (Rosetta Biosoftware) to process data analysis. The error model of Rosetta Resolver System® could remove both systematic and random errors form the data. We ﬁltered out spots that the ﬂag is less than 0. Spots that passed the criteria were normalized by 50% media scaling normalization method.Normalize intensities: Median scaling performed on data set without flagged and control data. Merge technical replicate data: Average intensity values calculated on technical replicates.  Calculate average ratios of the hybridization replicates and find significant values for each gene by pairwise comparision (Ranking and hypothesis testing).  Change in miRNA expression (log2 ratio) in calculated by the value in CPT-treated sample is compared with that in untreated sample.

source_name: glioblastoma

label_protocol: 1 µg of small RNA was reverse-transcribed and amplified using Amino Allyl aRNA Amplification Kit (Phalanx Biotech Group, Taiwan) and Cy5 dyes (Amersham Pharmacia, Piscataway, NJ, USA).

growth_protocol: U87-MG cells were maintained in Minimum essential Eagle medium (MEM) with 10% fetal bovine serum (Biological Industries, Cromwell, CT, USA), 100 units/ml penicillin, 100 μg/ml streptomycin, 1 mM sodium pyruvate, and 1 mM nonessential amino acids at 37 °C in a 5% CO2 incubator.

extract_protocol: Total RNA was respectively isolated from U87-MG cells with or without 200 ng/ml IGF-1 treatment by using Trizol reagent.  The small RNA were extracted from total RNA. The small RNAs were characterized by Agilent RNA 6000 Nano assay kit (Angilent Technologies, Santa Clara, CA, USA) to ensure good quality (OD260/OD280 >1.6; OD260/OD230 >1.0; RNA integrity number >5.0) for array analysis.

treatment_protocol: U87-MG cells were treated with or without 200 ng/ml IGF-1 for 48 h.

tag: cell line

value: control


title: G566 DNAm


title: IGF1-treated U87-MG Replicate 1

description: miRNAs from  IGF-treated U87-MG


title: G577 DNAm


title: CH OA 4

description: osteoarthritic CH tissue


title: U87-MG Replicate 1

description: miRNAs from  U87-MG


title: cox4d _t_46


title: IGF1-treated U87-MG Replicate 2

description: miRNAs from  IGF-treated U87-MG


title: ND015


title: G583 DNAm


title: CH OA 3

description: osteoarthritic CH tissue


title: cox4d _t_32


title: G620 DNAm


title: ND011


title: cox4d _t_24


title: G584 DNAm


title: G567 DNAm


title: cox4d _t_22


title: CH OA 1

description: osteoarthritic CH tissue


title: ND012


title: ND010


title: G799 DNAm


title: CH OA 2

description: osteoarthritic CH tissue


title: cox4d _t_18


title: G523 DNAm


title: G564 DNAm


title: G571 DNAm


title: cox4d _t_16


title: ND009


title: cox4d _t_15


title: CH ctrl 4

description: control


title: CH ctrl 3

description: control


title: cox4d _t_14


title: ND007


title: G411 DNAm


title: cox4d _t_11


title: cox4d _t_13


title: G489 DNAm


title: ND005


title: G551 DNAm


title: ND006


title: cox4d _t_10


title: G594 DNAm


title: ND003


title: cox4d _t_9


title: CH ctrl 2

description: control


title: CH ctrl 1

description: control


title: CH OA 5

description: osteoarthritic CH tissue


title: cox4d _t_38


title: OC-C OA 5

description: osteoarthritic OC cartilage


title: cox4d _t_7


title: G498 DNAm


title: cox4d _t_8


title: G361 DNAm


title: ND013


title: OC-C OA 4

description: osteoarthritic OC cartilage


title: cox4d _t_4


title: OC-C OA 3

description: osteoarthritic OC cartilage


title: cox4d _t_2


title: cox4d _t_0


title: OC-C OA 2

description: osteoarthritic OC cartilage


title: TP35

city: Cincinnati

first: Timothy

last: Phoenix

state: OH

address: 231 Albert Sabin Way, MSB 3005M

department: Division of Pharmaceutical Sciences

institute: University of Cincinnati

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq
fastq seqences were aligned to mm10 using Tophat
number of reads was calculated for each Entrez gene
differential expression analysis was performed using edgeR
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited raw counts with genes in rows and samples in columns

source_name: Primary mouse tumor cell line

growth_protocol: GFP-positive regions of primary mouse tumor samples were microdissected and frozen on dry ice. Primary tumor cell lines were grown in neural stem cell (neurosphere) media containing Neurobasal media + Glutamax + Penn/Strep + NaPyr + N2 + B27 + bFGF + EGF

extract_protocol:
RNA was isolated using the NucleoSpin RNA kit (Macherey-Nagel) and processed as per manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: background strain

value: Cortical


title: TP33


title: OC-C OA 1

description: osteoarthritic OC cartilage


title: ND001


title: cox4d _t_6


title: TP11

source_name: Mouse brainstem tissue

value: WT

value: Brainstem


title: OC-C ctrl 5

description: control


title: OC-C ctrl 4

description: control


title: Sample 1_Vagal_WholeNodoseSeq_10X

description:
Vagal_WholeNodoseSeq_filtered.mtx, Vagal_WholeNodoseSeq_raw.mtx
This sample (GSM) represents a pool of single cells processed with the 10X Genomics technology.

value: nodose ganglion

value: post natal 6 weeks


title: cox4d _t_5


title: OC-C ctrl 3

description: control


title: TP23

source_name: Primary mouse tumor


title: OC-C ctrl 2

description: control


title: nde1d nde2d ndi1d _t_58

value: nde1{delta} nde2{delta} ndi1{delta}


title: nde1d nde2d ndi1d _t_38


title: nde1d nde2d ndi1d _t_32


title: nde1d nde2d ndi1d _t_46


title: nde1d nde2d ndi1d _t_24


title: nde1d nde2d ndi1d _t_18


title: nde1d nde2d ndi1d _t_20


title: nde1d nde2d ndi1d _t_28


title: nde1d nde2d ndi1d _t_15


title: TP10


title: nde1d nde2d ndi1d _t_16


title: nde1d nde2d ndi1d _t_22


title: TP22


title: OC-C ctrl 1

description: control


title: nde1d nde2d ndi1d _t_13


title: nde1d nde2d ndi1d _t_12


title: nde1d nde2d ndi1d _t_14


title: TP21


title: CH 5

description: monophasic chondral tissue


title: G549 DNAm


title: cox4d _t_28


title: TP20


title: nde1d nde2d ndi1d _t_9


title: cox4d _t_20


title: nde1d nde2d ndi1d _t_10


title: TP12


title: CH 4

description: monophasic chondral tissue


title: nde1d nde2d ndi1d _t_11


title: CH 3

description: monophasic chondral tissue


title: CH 1

description: monophasic chondral tissue


title: TP17


title: nde1d nde2d ndi1d _t_2


title: nde1d nde2d ndi1d _t_0


title: TP19


title: nde1d nde2d ndi1d _t_8


title: TP16


title: nde1d nde2d ndi1d. _t_5


title: nde1d nde2d ndi1d _t_7


title: OC-C 5

description: biphasic osteochondral tissue


title: TP18


title: wt_t_58


title: wt_t_46


title: TP15


title: wt_t_38


title: OC-C 4

description: biphasic osteochondral tissue


title: TP14


title: OC-C 3

description: biphasic osteochondral tissue


title: CH 2

description: monophasic chondral tissue


title: TP13


title: wt_t_24


title: nde1d nde2d ndi1d _t_4


title: wt_t_22


title: OC-C 2

description: biphasic osteochondral tissue


title: nde1d nde2d ndi1d _t_6


title: wt_t_20


title: Control_replicate 2

city: Mumbai

first: Ullas

middle: Kolthur

last: Seetharam

state: Maharashtra

address: Homi Bhabha Road, Colaba

department: Department of Biological Sciences

country: India

institute: Tata Institute of Fundamental Research

description: miRNA

data_processing:
Illumina Casava1.8.2 software used for basecalling.
The raw reads were pre-processed to remove poor quality bases using Cutadapt v1.5  with parameter -q 20, adapter contaminants using Cutadapt v1.5 as reported by FastQC v0.11.2, trim poly A/T, ambiguous nucleotides (represented by N) from both ends and low-complexity regions using prinseq-lite-0.20.4. Reads with length less than 15 bases or more than 35 bases were discarded. Duplicate reads were removed from pre-processed reads.
The unique reads were kept along with their frequency information (raw read count) for further downstream analysis. These reads were mapped on mouse genome assembly GRCm38 (GenBank assembly ID GCA_000001635.2) using Bowtie v1.0.1 with maximum allowed mismatch of 2 bases. Reads mapped to multiple genomic loci were rescued using MuMRescueLite v090522.
Genome_build: mm10

source_name: Liver

extract_protocol:
Liver from animals was dissected out, flash frozen in Liq. Nitrogen, and RNA was isolated using Trizol reagent.
1 ug of total RNA was used for the construction of sequencing libraries. Tru Seq Small RNA sample preparation kit v2 (Catalog No.: RS-200-0036) from Illumina, was used  according to manufacturer specified protocols. The library was then validated on the Agilent bioanalyzer using DNA High sensitivity chip.

treatment_protocol: Wild type Ad libitum fed C57BL/6 mice

value: 2-3 months

tag: paradigm

value: Ad Libitum Fed

value: Liver


title: wt_t_18


title: OC-C 1

description: biphasic osteochondral tissue


title: wt_t_15


title: wt_t_14


title: wt_t_16


title: rat hypoxia rep3

city: Woolloongabba

first: Inge

last: Seim

state: Queensland

address: 37 Kent St

country: Australia

institute: Queensland University of Technology

description: polyadenylated RNA

data_processing:
FASTQ files were aligned to rat (NCBI RGSC_v3.4) or NMR (UCSC hetGla2) genomes using Bowtie2 v2.1.0 [PMID 22388286] and the spliced-read mapper TopHat (v2.0.9) [PMID 23618408] and reference gene annotations to guide the alignment (-G argument in TopHat).
Fragments per kilobase of transcript per million mapped reads (FPKM) were calculated using a Cufflinks v2.1.1 [PMID 22383036], with default parameters.
Insert metrics of PE reads was obtained using picard-tools v1.137 [https://github.com/broadinstitute/picard].
Genome_build: rat NCBI RGSC_v3.4 and NMR UCSC hetGla2
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample (abundance measurements).

molecule: polyA RNA

organism: Rattus norvegicus

source_name: liver

extract_protocol:
Total RNA was isolated from frozen tissues using an RNAqueous kit (Life Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Rat and naked mole rats (NMR) were exposed to short-term hypoxia (8% oxygen) for 8 hours --the estimated oxygen condition in NMR tunnels.

value: liver

value: rat 8% O2 8 hours


title: Control_replicate 1

description: miRNA


title: Day 0 3

description: CH  day 0


title: wt_t_13


title: Day 0 2

description: CH  day 0


title: wt_t_32


title: Day 0 1

description: CH  day 0


title: wt_t_11


title: wt_t_12


title: wt_t_28


title: rat hypoxia rep1

description: polyadenylated RNA


title: CH 4

description: CH  day 29


title: CH ctrl 5

description: control


title: CH 3

description: CH  day 28


title: wt_t_5


title: wt_t_7


title: wt_t_6


title: wt_t_8


title: wt_t_2


title: CH 2

description: CH  day 28


title: cox4d _t_12


title: rat hypoxia rep2

description: polyadenylated RNA


title: wt_t_0


title: OC-B 4

description: OC  bottom component


title: cox4d_tco89d_t12_2

growth_protocol: 30 C ,200 RPM in YNB + NH4 + 2% glucose, 50 ml in 250 ml baffled shake  flask

extract_protocol:
total RNA was extracted and purified using Direct-zol™-96 MagBead RNA method from ZymoResearch
RNA-Seq libraries were prepared using purified RNA isolated as described above. RNA quality and concentration were assayed using a Fragment Analyzer instrument. RNA-seq libraries were prepared using the TruSeq Stranded mRNA PolyA (Unique Dual Index) kit paired with the Ribo-Zero rRNA removal kit (Illumina, San Diego, CA). Libraries were sequenced on an Illumina HiSeq 4000 instrument.

treatment_protocol: Samples were collected for RNA extractions by vacuum filtration onto nylon filters.Filters were immediately placed into 2 ml snap cap tubes, submerged into liquid nitrogen and stored at -80°C until RNA extraction. Sampling was at at t=0 hours (log phase), 12 and 16 hours as technical replicates.

value: cox4{delta} tco89{delta}


title: cox4d_tco89d_t16_1


title: cox4d_tco89d_t16_2


title: cox4d_tco89d_t12_1


title: wt_t_9


title: OC-B 3

description: OC  bottom component


title: wt_t_10


title: cox4d_tco89d_t0_2


title: OC-B 2

description: OC  bottom component


title: cox4d_tco89d_t0_1


title: cox4d_rts1d_t16_1

value: cox4{delta} rts1{delta}


title: OC-B 1

description: OC  bottom component

value: iPSCs-derived MSCs


title: CH 1

description: CH  day 28


title: cox4d_rts1d_t12_1


title: cox4d_rts1d_t12_2


title: wt_t_4


title: OC-T 4

description: OC top component


title: KOV54: Short-term Survivor (HG-U133_Plus_2)

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45 °C on GeneChip® Human Genome U133 plus 2.0 oligonucleotide microarray chips (Affymetrix, Inc., Santa Clara, CA, USA) following the manufacturer’s protocols. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

value: ovary

value: IV

value: high grade serous

value: platinum resistant


title: cox4d_rts1d_t0_1


title: KOV48: Short-term Survivor (HG-U133_Plus_2)

value: IIIC

value: platinum partially sensitive


title: KOV49: Short-term Survivor (HG-U133_Plus_2)


title: KOV40: Short-term Survivor (HG-U133_Plus_2)


title: KOV41: Short-term Survivor (HG-U133_Plus_2)


title: cox4d_ras2d_t16_2

value: cox4{delta} ras2{delta}


title: cox4d_ras2d_t16_1


title: OC-T 2

description: OC top component


title: cox4d_ras2d_t12_2


title: cox4d_ras2d_t12_1


title: cox4d_ras2d_t0_2


title: KOV32: Short-term Survivor (HG-U133_Plus_2)


title: OC-T 1

description: OC top component


title: cox4d_ras2d_t0_1


title: KOV43: Short-term Survivor (HG-U133_Plus_2)


title: G5-4

description: OM + 10 nM VitD3 + 100 ng/ml BMP-7(Dex0-14)


title: coq2d_tco89d_t16_2

value: coq2{delta} tco89{delta}


title: coq2d_tco89d_t16_1


title: coq2d_tco89d_t12_2


title: G5-3


title: cox4d_rts1d_t0_2


title: KOV16: Long-term survivor (HG-U133_Plus_2)

value: platinum sensitive


title: KOV11: Long-term survivor (HG-U133_Plus_2)


title: KOV9: Long-term survivor (HG-U133_Plus_2)


title: KOV34: Short-term Survivor (HG-U133_Plus_2)


title: coq2d_tco89d_t12_1


title: KOV8: Long-term survivor (HG-U133_Plus_2)

value: IIC


title: G5-2


title: coq2d_tco89d_t0_1


title: DS40M4-minus-IPTG-2

city: Bloomington

first: Julia

middle: C

last: van Kessel

state: IN

address: 1001 E 3rd Street

department: Biology

institute: Indiana University

data_processing:
Read sequences were de-multiplexed using bcl2fastq (software versions 2.1.0.31).
Sequencing reads were trimmed for quality and adapters using Trimmomatic (v0.33 for all samples except the DluxR ChIP H-NS samples which used v0.38) with the following parameters: ILLUMINACLIP:adapters.fa:3:20:6 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:30
Reads were mapped to the genome using bowtie2 (v2.3.4.3)
Read counts were determined for genes and intergenic regions using a custom perl script
Genome_build: Vibrio campbellii ATCC BAA-1116 with the refseq IDs NC_009783.1, NC_009784.1, and NC_009777.1
Genome_build: Vibrio campbellii strain DS40M4 with the refseq IDs CP030788.1, CP030789.1, CP030790.1
Supplementary_files_format_and_content: gene and region counts in tab-delimited file; regions IDs begin with the keyword "Inter". Regions contain "." separated elements: "Inter",MoleculeID,strand(0=top;1=bottom),start of intergenic region,interval(# of 100bp windows from start),MoleculeID. For example geneID Inter.CP030788.1.0.1009310.1.CP030788.1 describes a 100bp interval on the top strand starting at 1009410 and ending at 1009510.

organism: Vibrio campbellii

source_name: Bacterial lysate

growth_protocol: Cells were diluted to OD600=0.005 in LBv2 and grown at 30°C to an OD600 of 1.8

extract_protocol:
RNA was extracted using Trizol and chloroform
Total RNA was first treated with RiboMinus Transcriptome Isolation Kit (Bacteria) (ThermoFisher Scientific, cat#K155004) to remove excess ribosomal RNA
All libraries were prepared using ScriptSeq RNA-Seq Library Preparation kit (Illumina, cat#SSV21124) according to manufacturer’s protocol
For all samples, sequencing barcodes selected from TruSeq Dual Index Sequencing Primer Box, Paired-End (Illumina cat#PE-121-1003) were added to the libraries during construction for multiplexing. The barcoded libraries were cleaned with AMPure XP beads (Beckman Coulter, cat#A63882), verified using Qubit4 fluorometer (ThermoFisher Scientific) and 2200 TapeStation bioanalyzer (Agilent Technologies), then pooled
Pooled libraries were sequenced on Illumina NextSeq 500 (Illumina) with NextSeq75 High Output v2 kit (Illumina cat#FC-404-2005)
The Libraries were sequenced on paired-end 2x38 bp run

treatment_protocol: IPTG was added at 100 uM final concentration to appropriate cultures

value: wild-type, pMMB67EH-tfoX-kanR

value: No IPTG


title: G4-4

description: OM + 10 nM VitD3 + 100 ng/ml BMP-7


title: G5-1


title: coq2d_rts1dd_t16_2

value: coq2{delta} rts1d{delta}


title: coq2d_rts1dd_t16_1


title: KOV7: Long-term survivor (HG-U133_Plus_2)

source_name: ovarian cancer


title: coq2d_rts1dd_t12_2


title: coq2d_rts1dd_t12_1


title: G4-3

description: OM + 10 nM VitD3 + 100 ng/ml BMP-7


title: coq2d_rts1dd_t0_1


title: coq2d_rts1dd_t0_2


title: DS40M4-plus-IPTG-3

value: IPTG added


title: coq2d_ras2d_t16_2

value: coq2{delta} ras2{delta}


title: G4-1

description: OM + 10 nM VitD3 + 100 ng/ml BMP-7


title: DS40M4-plus-IPTG-2


title: coq2d_ras2d_t16_1


title: DS40M4-minus-IPTG-3


title: KOV46: Short-term Survivor (HG-U133_Plus_2)


title: OC-T 3

description: OC top component


title: coq2d_ras2d_t12_2


title: coq2d_tco89d_t0_2


title: G3-4

description: OM + 10 nM VitD3


title: DS40M4-plus-IPTG-1


title: coq2d_ras2d_t12_1


title: coq2d_ras2d_t0_1


title: BB120-minus-IPTG-3


title: coq2d_ras2d_t0_2


title: G3-3

description: OM + 10 nM VitD3


title: G3-2

description: OM + 10 nM VitD3


title: tco89d_t16_1


title: tco89d_t16_2


title: tco89d_t12_2


title: G3-1

description: OM + 10 nM VitD3


title: G4-2

description: OM + 10 nM VitD3 + 100 ng/ml BMP-7


title: tco89d_t0_2


title: BB120-minus-IPTG-1


title: tco89d_t0_1


title: G2-4

description: OM


title: DS40M4-minus-IPTG-1


title: BB120-plus-IPTG-2


title: rts1d_t16_2


title: rts1d_t16_1


title: G2-3

description: OM


title: rts1d_t12_2


title: rts1d_t12_1


title: G2-2

description: OM


title: rts1d_t0_2


title: BB120-minus-IPTG-2


title: ras2d_t16_1


title: rts1d_t0_1


title: G2-1

description: OM


title: G1-4

description: MM


title: ras2d_t16_2


title: tco89d_t12_1


title: G1-3

description: MM


title: ras2d_t12_1


title: ras2d_t12_2


title: BB120-plus-IPTG-3


title: ras2d_t0_2


title: G1-2

description: MM


title: cox4d_t16_2


title: ras2d_t0_1


title: G1-1

description: MM


title: BB120-plus-IPTG-1


title: cox4d_t16_1


title: CM+BMP6-4

description: optimal chondrogenic medium


title: cox4d_t12_2


title: CM+BMP6-3

description: optimal chondrogenic medium


title: cox4d_t12_1


title: CM+BMP6-2

description: optimal chondrogenic medium


title: MD_009: PL_2h_rep3

city: fukuoka nishi ward

first: Cunkuan

last: Shen

state: fukuoka

address: Motooka

country: Japan

institute: kyushu university

description: Gene expression of Salmonella cells after 2h Polylysine treatment

hyb_protocol: For hybridization, 600 ng of labelled cRNA was fragmented in a 25 uL reaction mixture containing uL 1× Agilent fragmentation buffer and  10× 5 uL blocking agent at 60°C for 30 min. Afterwards, 25 uL of 2× GEx hybridization buffer HI-RPM was added to the fragmented cRNA and hybridized onto the arrays at 65°C for 17 h in Agilent hybridization oven with rotation (10 rpm). Then, microarrays were washed using gene expression wash buffer 1 and 2 for 1 min each, followed by a few seconds of air-dry.

scan_protocol: Slides were scanned on the Agilent DNA Microarray Scanner with Sureelect High-resolution Technology (SG11350602) using one color scan setting for 8 × 15k array slides (Scan resolution 5 um, Dye channel is set to Green and Extended Dynamic Range of 0.1 at 16-bit dynamic range 16-bit).

data_processing: Raw microarray data were extracted from scanned images by using Agilent Feature Extraction (FE) software (version 10.7.3.1), and then exported to GeneSpring GX 13.0 version software (Agilent). Log2 fluorescence ratios were generated for each replicate spot and averaged. The expression fold change of a given gene was calculated as the ratio of the signal intensity of the test sample to the signal intensity of the control sample. Significance of these expression values was determined with P values of ≤0.05. The transcripts of predominantly upregulated or downregulated genes were identified using a ≥ 2- fold expression cutoff.

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: Salmonella cells, Polylysine treated, 2h, replicate3

label_protocol: Two-hundreds ng of purified total RNA were used to produce Cyanine 3-CTP dye labelled cRNA using the Quick Amp Labeling kit, and then purified with the RNeasy Mini Kit (Qiagen).

extract_protocol: Salmonella cells attached on petri-dishes were scrubbed with spreading rod and mixed with the planktonic cells. The cell suspension was transferred into 50 mL conical centrifuge tube. The cells were collected by centrifugation at 5,800 × g for 10 min at room temperature. The quantity of RNA was determined using a NanoDrop ND-1000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA). RNA samples were further purified using RNase-free DNase I (Qiagen, Germany) and RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions. Quality of the total RNA was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). RNA samples were stored at -80°C until further use.

treatment_protocol: Overnight culture of S. Typhimurium NBRC 12529 was harvested by centrifugation at 3,300  × g at 4°C for 15 min, followed by dilution in sterile water. ε-Polylysine (Chisso Corporation, Tokyo, Japan) was dissolved in water at 0.002% and filter-sterilized with EB-DISK 25 (pore size 0.2 μm, Kanto Chemical Co., Ltd., Tokyo, Japan). Five mL of 0.2% Bacto Soytone and 5 mL of 0.002% ε-Polylysine were added into test tubes, for the control sample, 5 mL sterile water was added instead of ε-Polylysine. Then, Salmonella cell suspension was added to the tubes and the optical density at 660 nm (OD660) of suspensions was adjusted to around 0.7, corresponding to 109 – 1010 CFU/ml. Finally, solutions in the tubes were poured into to petri-dishes and incubated at 30°C for 2 h.


title: cox4d_t0_2


title: MD_007: PL_2h_rep1

source_name: Salmonella cells, Polylysine treated, 2h, replicate1


title: MD_006: Control_2h_rep3

description: Gene expression of Salmonella cells after 2h adhesion

source_name: Salmonella cells, untreated, 2h, replicate3


title: MD_008: PL_2h_rep2

source_name: Salmonella cells, Polylysine treated, 2h, replicate2


title: MD_005: Control_2h_rep2

source_name: Salmonella cells, untreated, 2h, replicate2


title: MD_003: Control_0h_rep3

description: Gene expression of Salmonella cells without treatment

source_name: Salmonella cells, untreated, replicate3


title: MD_004: Control_2h_rep1

source_name: Salmonella cells, untreated, 2h, replicate1


title: CM-4

description: chondrogenic medium

source_name: iMPCs


title: cox4d_t0_1

source_name: Saccharomyces cerevisiae


title: TB3 48h

city: Hohhot

first: Wei

last: Zhang

state: Inner Mongolia

address: Zhaowuda Road

country: China

institute: Inner Mongolia Agricultural University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter,poly-N and low quality reads.
Index of the reference genome was built using Bowtie V2.2.3 and paired-end clean reads were aligned to the reference genome using Tophat V2.0.12.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene considering the effect of sequencing depth and gene length for the reads count at the same time, and the most commonly used method for estimating gene expression levels
Genome_build: Duddingtonia flagrans CIM1 (Accession number: MDKD00000000)
Supplementary_files_format_and_content: FPKM values and readcounts for all samples

organism: Arthrobotrys flagrans

source_name: Hyphal cells

growth_protocol: 28℃, Corn meal agar

extract_protocol:
Cells were removed, flash frozen in  liquid nitrogen, and RNA was harvested using RNAprep Pure Plant Kit of TIANGEN BIOTECH.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Treatment with extraction of Caenorhabditis elegans for 0h, 12h, 48h, respectively.

tag: developmental stage

value: Hyphae

value: Hyphal cells


title: MD_002: Control_0h_rep2

source_name: Salmonella cells, untreated, replicate2


title: jmj17-1_4d+8h_R1

first: Wan-Sheng

last: Lo

state: Taiwan

address: 128 Academia Road, Section 2, Nankang

department: IPMB

institute: Academia Sinica

hyb_protocol: Affymetrix® GeneChip® Fluidics Station 450

scan_protocol: Affymetrix GeneChip® Scanner 3000

data_processing: The data were analyzed with  GeneChip Operation System 1.4 (GCOS 1.4)

organism: Arabidopsis thaliana

source_name: Whole seedling

label_protocol: GeneChip® Hybridization Oven 640

growth_protocol: Seeds of each genotypes were grown in 1/2MS without sucrose media containing plates for 4days dark followed by 2,4 and 8 hours of light

extract_protocol: Total RNA from   Col-0 and jmj17-1 seedling was isolated using RNeasy Plant Mini Kit (QIAGEN), Cat. No. 74904

treatment_protocol: 4days dark (4d); 4days dark+2h light (4d+2h),   4days dark+4h light (4d+4h),  and 4days dark+8h light (4d+8h),

value: Whole seedling

tag: ecotype

value: Col-0 background

value: jmj17-1 (mutant)

value: 4days dark+8h light (4d+8h)


title: jmj17-1_4d+8h_R2


title: TB2 48h

tag: strain


title: MD_001: Control_0h_rep1

source_name: Salmonella cells, untreated, replicate1


title: CM-3

description: chondrogenic medium

value: iPSCs-derived MSCs


title: coq2d_t16_2


title: WT_4d+8h_R2

value: Wild type (WT)

tag: treatment


title: coq2d_t16_1


title: TB1 48h


title: jmj17-1_4d+4h_R2

value: 4days dark+4h light (4d+4h)


title: jmj17-1_4d+4h_R1


title: CM-2

description: chondrogenic medium


title: WT_4d+4h_R1


title: TA3 12h


title: CM+BMP6-1

description: optimal chondrogenic medium


title: WT_4d+4h_R2


title: coq2d_t12_2


title: CM-1

description: chondrogenic medium


title: BM-4

description: control


title: coq2d_t12_1


title: TA1 12h


title: coq2d_t0_2


title: coq2d_t0_1


title: TA2 12h


title: BM-3

description: control


title: C2 0h


title: BM-1

description: control


title: BM-2

description: control


title: wt_t16_2


title: C1 0h


title: WT_4d+8h_R1


title: C3 0h


title: wt_t16_1


title: jmj17-1_4d+2h_R2

value: 4days dark+2h light (4d+2h)


title: wt_t12_2


title: ΔprpD-2

city: Wuhan

first: Xinfeng

last: Li

address: Shi zi shan street

institute: Huazhong Agricultural University

data_processing:
The quality of the raw sequence data were first assessed by FastQC and the sequences were then filtered and trimmed by Trimmomatic
The remaining reads were used to map to the reference genome of B. thuringiensis by Bowtie2
Alignments reported from Bowtie2 were further processed by the BEDTools software
Differential expression of all of transcripts was quantified through DEGseq software
Differential expressed genes were simply defined as at least 2-fold change with FDR (false discovery rate) less than 0.001.
Genome_build: B. thuringiensis BMB171
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Bacillus thuringiensis BMB171

source_name: bacteria

growth_protocol: Bacteia were growth in GYS medium with initial OD600=0.01

extract_protocol:
Bacteria were lysed by constantly grinding in the presence of liquid nitrogen with the total RNA extracted using TRIzol reagent (Invitrogen), and finally dissolved in 50 μL RNase-free water.
The total RNA quality was evaluated after ribosomal RNAs were removed. The RNA was then fragmented and used as a template for a randomly primed PCR. Strand-specific cDNA libraries were prepared by standard techniques for subsequent Illumina sequencing (Illumina HiSeq 2000)

value: delta-prpD


title: ΔprpD-1


title: BPA Female

city: Pathumwan

first: Surangrat

last: Thongkorn

state: Bangkok

address: Rama I

country: Thailand

institute: Chulalongkorn University

data_processing:
The library is sequenced using Illumina HiSeq 4000.
The sequence was filtered low-quality, adaptor-polluted and high content of unknown base(N) reads to get clean reads, then mapped with rn6 genome using HISAT software v0.1.6-beta with parameters --phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000.
For gene expression analysis, clean reads were mapped to reference using  Bowtie2 v2.2.5 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant  -p 1 -k 200, and then calculate gene expression level with RSEM, which is software for estimating gene and isoform expression levels from RNA-Seq data. With mapping result, we calculated reads coverage and reads distribution on transcripts. We then calculated statistcal analyses using pearson correlation between all samples.
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include expression profiles for each Sample .

source_name: neonatal rat hippocampus maternally exposed to BPA

extract_protocol:
Neonatal rat hippocampus was quickly removed in cold buffer and collected in RNAlater until use. RNA was extracted using mirVana miRNA Isolation Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Pregnant female rat at gestation day 1 (GD1) were daily treated with 5,000 µg/kg·BW or vehicle control until parturition.

value: Wistar

tag: Sex

value: female

value: maternally exposed to BPA

tag: age

value: postnatal day 1

value: hippocampus


title: jmj17-1_4d+2h_R1

tag: tissue

tag: genotype


title: WT_4d+2h_R1


title: wt_t12_1


title: BMB171-2

value: wild type


title: wt_t0_2


title: BPA Male

value: male


title: Vehicle control Female

source_name: neonatal rat hippocampus maternally exposed to vehicle

value: maternally exposed to vehicle (control)


title: jmj17-1_4d_R3

value: Whole seedling

value: 4days dark (4d)


title: wt_t0_1


title: jmj17-1_4d_R2

value: Col-0 background

value: jmj17-1 (mutant)


title: Vehicle control Male


title: BMB171-1


title: Splenic B cells, male late disease mouse 1

status: Public on Nov 13 2019

city: Philadelphia

first: Montserrat

last: Anguera

address: 3800 Spruce Street, Rosenthal Room 390EB

department: Biomedical Sciences

institute: University of Pennsylvania School of Veterinary Medicine

description:
mLateRNA_1
NZBW_Txi_counts.csv (column 4)

data_processing:
Reads aligned to mouse genome using Kallisto
Reads imported into R using tximport
Filtered for cpm>1
Passed through DESeq2, FDR < 0.05
Genome_build: Ensembl release GRCm38.p6
Supplementary_files_format_and_content: NZBW_Txi_counts.csv: all gene counts pre-filtering, generated using tximport

source_name: Splenic B cells

extract_protocol:
Spleens were isolated from late stage NZB/W F1 mice, B cells were isolated through positive-selection column, stimulated in culture for 24hrs with CpG
Library constructed following standard Illumina protocol

value: NZB/W F1

tag: disease state

value: lupus-like disease

tag: disease stage

value: late

value: CpG 24hrs

tag: gender

value: Splenic B cells


title: Splenic B cells, male late disease mouse 3

description:
mLateRNA_3
NZBW_Txi_counts.csv (column 6)

tag: cell type


title: Splenic B cells, female late disease mouse 2

description:
fLateRNA_2
NZBW_Txi_counts.csv (column 2)


title: jmj17-1_4d_R1


title: Splenic B cells, female late disease mouse 1

description:
fLateRNA_1
NZBW_Txi_counts.csv (column 1)


title: Splenic B cells, male late disease mouse 2

description:
mLateRNA_2
NZBW_Txi_counts.csv (column 5)


title: WT_4d_R2

value: Wild type (WT)


title: WT_4d_R3


title: WT_4d+2h_R2

value: 4days dark+2h light (4d+2h)


title: HD_Tonsil_2

first: Anthony

middle: Richard

last: Cillo

address: The Assembly, Room 4070C Bay 10, 5051 Centre Ave

department: Immunology

data_processing:
Demultiplexing using CellRanger mkfastq
Alignment and generation of gene/barcode matrices using CellRanger count
Genome_build: GRCh38
Supplementary_files_format_and_content: files containing gene/barcode matrices

source_name: tonsil tissue

extract_protocol: 10x 3' v2 scRNAseq

treatment_protocol: Ficoll density gradient centrifugation to isolate peripheral blood mononuclear cells from whole blood; mechanical distruption of tissues; live CD45+ single cells were sorted from all samples using a Beckman Coulter MoFlo Astrios.

value: tonsil tissue

value: Healthy donor


title: HD_PBMC_3

source_name: peripheral blood

value: peripheral blood


title: HD_Tonsil_4


title: HD_Tonsil_5


title: HD_PBMC_4


title: HD_PBMC_6


title: HD_Tonsil_1


title: HD_PBMC_2


title: HD_PBMC_5


title: HD_PBMC_1


title: HD_Tonsil_3


title: HNSCC_26_TIL

source_name: tumor tissue

value: tumor tissue

value: Head and neck squamous cell carcinoma (HNSCC)


title: HNSCC_25_PBMC


title: HNSCC_26_PBMC


title: HNSCC_24_TIL


title: HNSCC_23_PBMC


title: HNSCC_24_PBMC


title: HNSCC_25_TIL


title: HNSCC_23_TIL


title: Splenic B cells, female late disease mouse 3

description:
flateRNA_3
NZBW_Txi_counts.csv (column 3)

value: female


title: HNSCC_22_TIL


title: HNSCC_22_PBMC


title: WT_4d_R1

value: Whole seedling


title: HNSCC_20_PBMC


title: HNSCC_19_PBMC


title: HNSCC_19_TIL


title: HNSCC_18_TIL


title: HNSCC_17_TIL


title: HNSCC_20_TIL


title: HNSCC_12_PBMC


title: HNSCC_11_PBMC


title: HNSCC_17_PBMC


title: HNSCC_16_PBMC


title: HNSCC_11_TIL


title: HNSCC_16_TIL


title: HNSCC_12_TIL


title: HNSCC_18_PBMC


title: HNSCC_9_PBMC


title: HNSCC_8_TIL


title: HNSCC_9_TIL


title: HNSCC_10_PBMC


title: HNSCC_21_TIL


title: HNSCC_8_PBMC


title: HNSCC_6_PBMC


title: HNSCC_10_TIL


title: HNSCC_13_TIL


title: HNSCC_5_TIL


title: HNSCC_21_PBMC


title: HNSCC_6_TIL


title: HNSCC_5_PBMC


title: HNSCC_13_PBMC


title: HNSCC_2_TIL


title: HNSCC_4_TIL


title: HNSCC_3_PBMC


title: HNSCC_2_PBMC


title: HNSCC_7_TIL


title: HNSCC_1_PBMC


title: HNSCC_1_TIL


title: PSN4 HIV Positive ART Treatment Early (<6month)

city: Cleveland

first: Mark

last: Cameron

address: 10900 Euclid Ave

department: Population and Quantitative Health Sciences

institute: Case Western Reserve University

description:
rawCounts.csv
normalizedCounts.csv

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using skewer v0.2.2, then mapped to GRCh38 whole genome using Hisat2 v2.0.5
Read summarization was performed by the program featureCounts v1.5.0-p2 as part of the SubRead package using the NCBI Homo sapiens Annotation release 106.
Counts Per Million (CPM) values were generated through the edgeR Library v3.16.5 in R
Genome_build: GRCh38
Supplementary_files_format_and_content: rawCounts.csv: counts as generated by featureCounts, rows are gene features, columns are samples
Supplementary_files_format_and_content: normalizedCounts.csv: remove counts that were all zeroes (across the full set); Perform TMM normalization ; export log2(n+3) CPM

source_name: PBMC

growth_protocol: in vivo

extract_protocol:
RNA was extracted from 1 million PBMC using RNeasy Plus Mini Kit from QIAGEN
RNA libraries were prepared for sequencing using the Roche Kapa RNA hyper kit.

treatment_protocol: no treament

tag: hiv status

value: Positive

tag: treatment initiation

value: Early (<6month)


title: PSN6 HIV Positive ART Treatment Early (<6month)

description:
rawCounts.csv
normalizedCounts.csv


title: PSN28 HIV Positive ART Treatment Early (<6month)

description:
rawCounts.csv
normalizedCounts.csv


title: PSN25 HIV Positive ART Treatment Early (<6month)

description:
rawCounts.csv
normalizedCounts.csv


title: PSN23 HIV Positive ART Treatment Early (<6month)

description:
rawCounts.csv
normalizedCounts.csv


title: PSN1 HIV Positive ART Treatment Early (<6month)

description:
rawCounts.csv
normalizedCounts.csv


title: PSN14 HIV Positive ART Treatment Early (<6month)

description:
rawCounts.csv
normalizedCounts.csv


title: H045 HIV Positive ART Treatment Late (>12months)

description:
rawCounts.csv
normalizedCounts.csv

value: Late (>12months)


title: PSN12 HIV Positive ART Treatment Early (<6month)

description:
rawCounts.csv
normalizedCounts.csv


title: PSN10 HIV Positive ART Treatment Early (<6month)

description:
rawCounts.csv
normalizedCounts.csv


title: H002 HIV Positive ART Treatment Late (>12months)

description:
rawCounts.csv
normalizedCounts.csv


title: H084 HIV Positive ART Treatment Late (>12months)

description:
rawCounts.csv
normalizedCounts.csv


title: C018 HIV Negative ART Treatment NA

description:
rawCounts.csv
normalizedCounts.csv

value: Negative


title: H019 HIV Positive ART Treatment Late (>12months)

description:
rawCounts.csv
normalizedCounts.csv


title: C021 HIV Negative ART Treatment NA

description:
rawCounts.csv
normalizedCounts.csv


title: HNSCC_4_PBMC


title: HNSCC_3_TIL


title: C011 HIV Negative ART Treatment NA

description:
rawCounts.csv
normalizedCounts.csv


title: C015 HIV Negative ART Treatment NA

description:
rawCounts.csv
normalizedCounts.csv


title: C017 HIV Negative ART Treatment NA

description:
rawCounts.csv
normalizedCounts.csv


title: C003 HIV Negative ART Treatment NA

description:
rawCounts.csv
normalizedCounts.csv


title: PSN20 HIV Positive ART Treatment Early (<6month)

description:
rawCounts.csv
normalizedCounts.csv


title: Huh7_siLATS2_rep_2

city: Basel

first: Ravi Kiran Reddy

last: KALATHUR

state: Basel

address: Mattenstrasse 28

department: Departement Biomedizin

country: Switzerland

institute: University of Basel

data_processing:
Base calling was done using Illumina software.
Sequenced reads were mapped to hg19 version of human genome using RNA-STAR using parameters (outFilterMultimapNmax=10 and outFilterType="BySJout").
Counts are obtained using qcount in qusaR and CPM (counts per million) was computed for each sample
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files contain counts as CPM values for each sample.

source_name: HCC cell line

extract_protocol:
Total RNA was isolated from 3 different cell lines in 3 replicates each using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction.
RNA quality control was performed with Bioanalyzer 2100 (Agilent) using the Eukaryote Total RNA Nano analysis kit from Labgene and RNA concentration was measured by Quanti-iTTM RiboGreen RNA assay kit (Thermo Fisher Scientific).
200ng of RNA was utilized for library preparation with the TruSeq Stranded total RNA kit plus Ribozero Gold (Illumina). The library quality check was performed using the DNF-473-33 - SS NGS Fragment analysis kit (Advanced Analytical Technologies Inc).

treatment_protocol: siRNA was transfected with RNAiMAX. RNAs from transfected Huh7 cells were harvested 48 hours after transfection.

tag: cell line

value: hepatocellular carcinoma cell line

tag: sirna


title: Huh7_siLATS2_rep_1


title: PSN22 HIV Positive ART Treatment Early (<6month)

description:
rawCounts.csv
normalizedCounts.csv


title: H042 HIV Positive ART Treatment Late (>12months)

description:
rawCounts.csv
normalizedCounts.csv


title: Huh7_siLATS1_rep_3


title: Huh7_siControl_rep3

value: siControl


title: Huh7_siLATS1_rep_2


title: Huh7_siLATS1_rep_1


title: Huh7_siControl_rep1


title: PSN18 HIV Positive ART Treatment Early (<6month)

description:
rawCounts.csv
normalizedCounts.csv


title: Huh7_siLATS2_rep_3


title: X4315_2_1E6_A

city: Boston

first: Maria

last: Gutierrez-Arcelus

state: MA

address: 77 Avenue Louis Pasteur

department: Medicine

institute: Brigham and Women's Hospital, Harvard Medical School

data_processing:
We aligned reads to the hg19 reference genome with subread v1.5.1, requiring uniquely mapped reads.
We quantified gene expression levels with featureCounts, requiring a mapping quality of at least 20 and using Gencode v19 annotation.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files including gene counts, normalized gene expression (log2(tpm+1) expression values), metadata

source_name: TB03074315_CD4 memory T cells_2

extract_protocol:
Frozen PBMCs received from the Genotype and Phenotype (GaP) Registry at The Feinstein Institute for Medical Research, were thawed and CD4 memory T cells isolated with magnetic selection (Miltenyi isolation kit).
Illumina TruSeq™ stranded mRNA sample preparation kit
The 200 samples were prepared in 3 batches/plates.

tag: donor id

value: F

value: PBMCs

value: CD4 memory T cells

tag: time point

tag: replicate

value: A


title: X4401_0_1E6_A

source_name: TB03074401_CD4 memory T cells_0


title: X4315_48_1E6_A

source_name: TB03074315_CD4 memory T cells_48


title: X4401_8_1E6_A

source_name: TB03074401_CD4 memory T cells_8


title: X4401_12_1E6_A

source_name: TB03074401_CD4 memory T cells_12


title: X4401_4_1E6_A

source_name: TB03074401_CD4 memory T cells_4


title: X4315_8_1E6_A

source_name: TB03074315_CD4 memory T cells_8


title: X4315_24_1E6_A

source_name: TB03074315_CD4 memory T cells_24


title: X4401_48_1E6_A

source_name: TB03074401_CD4 memory T cells_48


title: X4315_4_1E6_A

source_name: TB03074315_CD4 memory T cells_4


title: X4306_8_1E6_A

source_name: TB03074306_CD4 memory T cells_8

value: M


title: X4306_24_1E6_A

source_name: TB03074306_CD4 memory T cells_24


title: X4306_0_1E6_A

source_name: TB03074306_CD4 memory T cells_0


title: X4401_72_1E6_A

source_name: TB03074401_CD4 memory T cells_72


title: Huh7_siControl_rep2


title: X4306_72_1E6_A

source_name: TB03074306_CD4 memory T cells_72


title: X4315_72_1E6_A

source_name: TB03074315_CD4 memory T cells_72


title: X4192_8_1E6_A

source_name: TB03074192_CD4 memory T cells_8


title: X4401_24_1E6_A

source_name: TB03074401_CD4 memory T cells_24


title: X4306_4_1E6_A

source_name: TB03074306_CD4 memory T cells_4


title: X4192_2_1E6_A

source_name: TB03074192_CD4 memory T cells_2


title: X4192_24_1E6_A

source_name: TB03074192_CD4 memory T cells_24


title: X4192_4_1E6_A

source_name: TB03074192_CD4 memory T cells_4


title: X4192_48_1E6_A

source_name: TB03074192_CD4 memory T cells_48


title: X4315_0_1E6_A

source_name: TB03074315_CD4 memory T cells_0


title: X4192_0_1E6_A

source_name: TB03074192_CD4 memory T cells_0


title: X4401_2_1E6_A

source_name: TB03074401_CD4 memory T cells_2


title: X3852_8_1E6_A

source_name: TB03073852_CD4 memory T cells_8


title: X4192_72_1E6_A

source_name: TB03074192_CD4 memory T cells_72


title: X3852_48_1E6_A

source_name: TB03073852_CD4 memory T cells_48


title: X3852_2_1E6_A

source_name: TB03073852_CD4 memory T cells_2


title: X3798_48_1E6_A

source_name: TB03073798_CD4 memory T cells_48


title: X3798_4_1E6_B

source_name: TB03073798_CD4 memory T cells_4

value: B


title: X3798_2_1E6_A

source_name: TB03073798_CD4 memory T cells_2


title: X3798_24_1E6_B

source_name: TB03073798_CD4 memory T cells_24


title: X3852_72_1E6_A

source_name: TB03073852_CD4 memory T cells_72


title: X3798_72_1E6_B

source_name: TB03073798_CD4 memory T cells_72


title: X3798_8_1E6_A

source_name: TB03073798_CD4 memory T cells_8


title: H020 HIV Positive ART Treatment Late (>12months)

description:
rawCounts.csv
normalizedCounts.csv

source_name: PBMC


title: X3798_8_1E6_B


title: X3852_4_1E6_A

source_name: TB03073852_CD4 memory T cells_4


title: X3798_4_1E6_A


title: X3798_12_1E6_B

source_name: TB03073798_CD4 memory T cells_12


title: X3798_12_1E6_A


title: X3798_2_1E6_B


title: X3798_24_1E6_A


title: X3591_4_1E6_A

source_name: TB03073591_CD4 memory T cells_4


title: X3591_72_1E6_A

source_name: TB03073591_CD4 memory T cells_72


title: X3591_48_1E6_A

source_name: TB03073591_CD4 memory T cells_48


title: X3798_0_1E6_A

source_name: TB03073798_CD4 memory T cells_0


title: X3591_2_1E6_A

source_name: TB03073591_CD4 memory T cells_2


title: X3852_24_1E6_A

source_name: TB03073852_CD4 memory T cells_24


title: X3852_12_1E6_A

source_name: TB03073852_CD4 memory T cells_12


title: X3591_24_1E6_A

source_name: TB03073591_CD4 memory T cells_24


title: X3798_72_1E6_A


title: X3798_0_1E6_B


title: X3591_0_1E6_A

source_name: TB03073591_CD4 memory T cells_0


title: X3577_8_1E6_A

source_name: TB03073577_CD4 memory T cells_8


title: X3577_48_1E6_A

source_name: TB03073577_CD4 memory T cells_48


title: X3577_4_1E6_A

source_name: TB03073577_CD4 memory T cells_4


title: X3591_8_1E6_A

source_name: TB03073591_CD4 memory T cells_8


title: X3852_0_1E6_A

source_name: TB03073852_CD4 memory T cells_0


title: X2608_48_1E6_A

source_name: TB03072608_CD4 memory T cells_48


title: X2608_2_1E6_A

source_name: TB03072608_CD4 memory T cells_2


title: X2608_8_1E6_A

source_name: TB03072608_CD4 memory T cells_8


title: X2608_4_1E6_A

source_name: TB03072608_CD4 memory T cells_4


title: X1936_72_1E6_A

source_name: TB03071936_CD4 memory T cells_72


title: X3577_24_1E6_A

source_name: TB03073577_CD4 memory T cells_24


title: X3577_72_1E6_A

source_name: TB03073577_CD4 memory T cells_72


title: X1936_8_1E6_A

source_name: TB03071936_CD4 memory T cells_8


title: X2608_0_1E6_A

source_name: TB03072608_CD4 memory T cells_0


title: X2608_72_1E6_A

source_name: TB03072608_CD4 memory T cells_72


title: X1936_2_1E6_A

source_name: TB03071936_CD4 memory T cells_2


title: X1936_4_1E6_A

source_name: TB03071936_CD4 memory T cells_4


title: X1936_12_1E6_A

source_name: TB03071936_CD4 memory T cells_12


title: X1936_0_1E6_A

source_name: TB03071936_CD4 memory T cells_0


title: X1454_8_1E6_A

source_name: TB03071454_CD4 memory T cells_8


title: X2608_24_1E6_A

source_name: TB03072608_CD4 memory T cells_24


title: X3577_12_1E6_A

source_name: TB03073577_CD4 memory T cells_12


title: X1454_4_1E6_A

source_name: TB03071454_CD4 memory T cells_4


title: X1936_24_1E6_A

source_name: TB03071936_CD4 memory T cells_24


title: X1454_72_1E6_A

source_name: TB03071454_CD4 memory T cells_72


title: X1454_48_1E6_A

source_name: TB03071454_CD4 memory T cells_48


title: X3577_0_1E6_A

source_name: TB03073577_CD4 memory T cells_0


title: X1454_2_1E6_A

source_name: TB03071454_CD4 memory T cells_2


title: X1454_0_1E6_A

source_name: TB03071454_CD4 memory T cells_0


title: X3577_2_1E6_A

source_name: TB03073577_CD4 memory T cells_2


title: X0641_72_1E6_A

source_name: TB03070641_CD4 memory T cells_72


title: X0641_8_1E6_A

source_name: TB03070641_CD4 memory T cells_8


title: X1454_12_1E6_A

source_name: TB03071454_CD4 memory T cells_12


title: X0641_48_1E6_A

source_name: TB03070641_CD4 memory T cells_48


title: X0641_4_1E6_A

source_name: TB03070641_CD4 memory T cells_4


title: X0641_2_1E6_A

source_name: TB03070641_CD4 memory T cells_2


title: X1936_48_1E6_A

source_name: TB03071936_CD4 memory T cells_48


title: X0641_24_1E6_A

source_name: TB03070641_CD4 memory T cells_24


title: X0514_8_1E6_A

source_name: TB03070514_CD4 memory T cells_8


title: X0641_12_1E6_A

source_name: TB03070641_CD4 memory T cells_12


title: X0514_72_1E6_A

source_name: TB03070514_CD4 memory T cells_72


title: X0641_0_1E6_A

source_name: TB03070641_CD4 memory T cells_0


title: X0514_4_1E6_A

source_name: TB03070514_CD4 memory T cells_4


title: X0514_48_1E6_A

source_name: TB03070514_CD4 memory T cells_48


title: X0514_2_1E6_A

source_name: TB03070514_CD4 memory T cells_2


title: X0514_12_1E6_A

source_name: TB03070514_CD4 memory T cells_12


title: X0514_24_1E6_A

source_name: TB03070514_CD4 memory T cells_24


title: X4749_72_1E6_A

source_name: TB03074749_CD4 memory T cells_72


title: X1454_24_1E6_A

source_name: TB03071454_CD4 memory T cells_24


title: X4749_8_1E6_A

source_name: TB03074749_CD4 memory T cells_8


title: X4749_48_1E6_A

source_name: TB03074749_CD4 memory T cells_48


title: X4749_2_1E6_A

source_name: TB03074749_CD4 memory T cells_2


title: X4749_4_1E6_A

source_name: TB03074749_CD4 memory T cells_4


title: X3798_48_1E6_B

source_name: TB03073798_CD4 memory T cells_48


title: X4218_72_1E6_A

source_name: TB03074218_CD4 memory T cells_72


title: X4749_0_1E6_A

source_name: TB03074749_CD4 memory T cells_0


title: X4218_24_1E6_A

source_name: TB03074218_CD4 memory T cells_24


title: X4749_24_1E6_A

source_name: TB03074749_CD4 memory T cells_24


title: X4218_4_1E6_A

source_name: TB03074218_CD4 memory T cells_4


title: X4218_12_1E6_A

source_name: TB03074218_CD4 memory T cells_12


title: X4218_0_1E6_A

source_name: TB03074218_CD4 memory T cells_0


title: X4178_72_1E6_A

source_name: TB03074178_CD4 memory T cells_72


title: X4178_48_1E6_A

source_name: TB03074178_CD4 memory T cells_48


title: X4178_8_1E6_A

source_name: TB03074178_CD4 memory T cells_8


title: X0514_0_1E6_A

source_name: TB03070514_CD4 memory T cells_0


title: X4178_24_1E6_A

source_name: TB03074178_CD4 memory T cells_24


title: X2608_12_1E6_A

source_name: TB03072608_CD4 memory T cells_12


title: X4178_12_1E6_A

source_name: TB03074178_CD4 memory T cells_12


title: X4157_48_1E6_A

source_name: TB03074157_CD4 memory T cells_48


title: X4178_0_1E6_A

source_name: TB03074178_CD4 memory T cells_0


title: X4157_8_1E6_A

source_name: TB03074157_CD4 memory T cells_8


title: X4157_2_1E6_A

source_name: TB03074157_CD4 memory T cells_2


title: X4157_4_1E6_A

source_name: TB03074157_CD4 memory T cells_4


title: X4157_24_1E6_A

source_name: TB03074157_CD4 memory T cells_24


title: X4218_48_1E6_A

source_name: TB03074218_CD4 memory T cells_48


title: X4157_0_1E6_A

source_name: TB03074157_CD4 memory T cells_0


title: X4092_8_1E6_A

source_name: TB03074092_CD4 memory T cells_8


title: X4218_2_1E6_A

source_name: TB03074218_CD4 memory T cells_2


title: X4092_72_1E6_A

source_name: TB03074092_CD4 memory T cells_72


title: X4749_12_1E6_A

source_name: TB03074749_CD4 memory T cells_12


title: X4178_2_1E6_A

source_name: TB03074178_CD4 memory T cells_2


title: X4218_8_1E6_A

source_name: TB03074218_CD4 memory T cells_8


title: X4178_4_1E6_A

source_name: TB03074178_CD4 memory T cells_4


title: X4092_2_1E6_A

source_name: TB03074092_CD4 memory T cells_2


title: X3878_72_1E6_A

source_name: TB03073878_CD4 memory T cells_72


title: X3878_8_1E6_A

source_name: TB03073878_CD4 memory T cells_8


title: X4092_0_1E6_A

source_name: TB03074092_CD4 memory T cells_0


title: X4092_4_1E6_A

source_name: TB03074092_CD4 memory T cells_4


title: X4092_12_1E6_A

source_name: TB03074092_CD4 memory T cells_12


title: X4157_72_1E6_A

source_name: TB03074157_CD4 memory T cells_72


title: X3878_4_1E6_A

source_name: TB03073878_CD4 memory T cells_4


title: X4092_48_1E6_A

source_name: TB03074092_CD4 memory T cells_48


title: X4157_12_1E6_A

source_name: TB03074157_CD4 memory T cells_12


title: X3878_48_1E6_A

source_name: TB03073878_CD4 memory T cells_48


title: X3878_24_1E6_A

source_name: TB03073878_CD4 memory T cells_24


title: X4092_24_1E6_A

source_name: TB03074092_CD4 memory T cells_24


title: X3878_0_1E6_A

source_name: TB03073878_CD4 memory T cells_0


title: X3703_72_1E6_A

source_name: TB03073703_CD4 memory T cells_72


title: X3703_8_1E6_A

source_name: TB03073703_CD4 memory T cells_8


title: X3703_4_1E6_A

source_name: TB03073703_CD4 memory T cells_4


title: X3703_2_1E6_A

source_name: TB03073703_CD4 memory T cells_2


title: X3189_4_1E6_A

source_name: TB03073189_CD4 memory T cells_4


title: X3189_72_1E6_A

source_name: TB03073189_CD4 memory T cells_72


title: X3703_0_1E6_A

source_name: TB03073703_CD4 memory T cells_0


title: X3189_8_1E6_A

source_name: TB03073189_CD4 memory T cells_8


title: X3703_24_1E6_A

source_name: TB03073703_CD4 memory T cells_24


title: X3189_48_1E6_A

source_name: TB03073189_CD4 memory T cells_48


title: X3189_2_1E6_A

source_name: TB03073189_CD4 memory T cells_2


title: X3878_2_1E6_A

source_name: TB03073878_CD4 memory T cells_2


title: X3189_24_1E6_A

source_name: TB03073189_CD4 memory T cells_24


title: X3189_12_1E6_A

source_name: TB03073189_CD4 memory T cells_12


title: X3148_72_1E6_A

source_name: TB03073148_CD4 memory T cells_72


title: X3189_0_1E6_A

source_name: TB03073189_CD4 memory T cells_0


title: X3148_8_1E6_A

source_name: TB03073148_CD4 memory T cells_8


title: X3148_4_1E6_A

source_name: TB03073148_CD4 memory T cells_4


title: X3148_24_1E6_A

source_name: TB03073148_CD4 memory T cells_24


title: X3148_48_1E6_A

source_name: TB03073148_CD4 memory T cells_48


title: X3148_2_1E6_A

source_name: TB03073148_CD4 memory T cells_2


title: X3878_12_1E6_A

source_name: TB03073878_CD4 memory T cells_12


title: X2560_8_1E6_B

source_name: TB03072560_CD4 memory T cells_8


title: X2560_72_1E6_A

source_name: TB03072560_CD4 memory T cells_72


title: X2560_8_1E6_A


title: X3148_0_1E6_A

source_name: TB03073148_CD4 memory T cells_0


title: X2560_72_1E6_B


title: X2560_4_1E6_A

source_name: TB03072560_CD4 memory T cells_4


title: X2560_48_1E6_B

source_name: TB03072560_CD4 memory T cells_48


title: X2560_48_1E6_A


title: X2560_2_1E6_B

source_name: TB03072560_CD4 memory T cells_2


title: X2560_2_1E6_A


title: X2560_24_1E6_A

source_name: TB03072560_CD4 memory T cells_24


title: X2560_24_1E6_B


title: X2560_12_1E6_B

source_name: TB03072560_CD4 memory T cells_12


title: X2560_12_1E6_A


title: X2560_0_1E6_B

source_name: TB03072560_CD4 memory T cells_0


title: X0100_8_1E6_A

source_name: TB03070100_CD4 memory T cells_8


title: X0100_72_1E6_A

source_name: TB03070100_CD4 memory T cells_72


title: X2560_0_1E6_A


title: X0100_4_1E6_A

source_name: TB03070100_CD4 memory T cells_4


title: X0100_24_1E6_A

source_name: TB03070100_CD4 memory T cells_24


title: X0100_12_1E6_A

source_name: TB03070100_CD4 memory T cells_12


title: X2560_4_1E6_B


title: X0100_48_1E6_A

source_name: TB03070100_CD4 memory T cells_48


title: X0100_0_1E6_A

source_name: TB03070100_CD4 memory T cells_0


title: Sample_MCF7_sgNT_Control_1

city: New York

first: Sagar

last: Chhangawala

state: NY

address: 1300 York Ave.

department: PBSB

institute: Weill Cornell Medical College

data_processing:
Raw reads were aligned using STAR (v2.5.0b, default parameters) to the hg38 genome.
Read counting was performed using htseq-count (v0.9.1, parameters: --stranded=no -t exon).
Genome_build: hg38
Supplementary_files_format_and_content: Tab delimited text file with Ensembl gene ID and counts for each gene

growth_protocol: MCF7 cells were obtained from ATCC and were cultured in DMEM/F-12 (Corning) and supplemented with 10% FBS, MEM non-essential amino acids (Corning), 50U/ml penicillin, and 50ng/ml streptomycin under normal oxygen conditions (5% CO2, 37 °C)

extract_protocol: RNA was extracted using the Rneasy Kit according to Manufactur's protocol.

value: Breast Cancer Cells

tag: sgguide

value: sgNT

tag: genotype/variation

value: Control


title: X3148_12_1E6_A

source_name: TB03073148_CD4 memory T cells_12

tag: Sex


title: Sample_MCF7_sgGFP_Control_1

value: sgGFP


title: Sample_MCF7_sg3_SMARCE1_2

value: SMARCE1 KO


title: Sample_MCF7_sgGFP_Control_2


title: Sample_MCF7_sg3_SMARCB1_1

value: SMARCB1 KO


title: Sample_MCF7_sg3_SMARCE1_1


title: Sample_MCF7_sgNT_Control_2


title: Sample_MCF7_sg2_SMARCE1_2


title: Sample_MCF7_sg2_SMARCB1_1


title: Sample_MCF7_sg2_SMARCB1_2


title: Sample_MCF7_sg3_SMARCB1_2


title: Sample_MCF7_sg1_SMARCB1_2


title: Sample_MCF7_sg2_SMARCE1_1


title: Sample_MCF7_sg1_SMARCB1_1


title: Sample_MCF7_sg1_SMARCE1_2


title: Sample_HCC70_sgGFP_Control_2


title: Sample_HCC70_sgNT_Control_1


title: Sample_HCC70_sgNT_Control_2


title: Sample_HCC70_sgGFP_Control_1


title: X0100_2_1E6_A

source_name: TB03070100_CD4 memory T cells_2

tag: age


title: Sample_HCC70_sg2_ARID1A_1

value: ARID1A KO


title: Sample_HCC70_sg2_ARID1A_2


title: Sample_HCC70_sg1_ARID1A_2


title: Sample_HCC70_sg1_ARID1A_1


title: Sample_BT549_sgGFP_Control_2


title: Sample_BT549_sgNT_Control_1


title: Sample_BT549_sgNT_Control_2


title: Sample_BT549_sgGFP_Control_1


title: Sample_BT549_sg1_ARID1A_1


title: Sample_DMSO_ET_KO_GRHL1_1

library_source: genomic

data_processing:
Raw reads were trimmed using trimmomatic (v0.35, Parameters: TruSeq3-PE adapters, LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36).
Each sample was aligned to hg38 genome using bowtie2 48 (v2.2.6, Parameters: -X2000 –local –mm --no-mixed --no-discordant).
Duplicate reads were then removed using MarkDuplicates (v2.9.0, REMOVE_DUPLICATES=True).
Peak calling was performed using MACS2 49 (v2.1.0, parameters: --keep-dup all -g hs -q 0.01).
BigWig tracks were generated using MACS2 and then scaled using rtracklayer (v1.40.6).
Genome_build: hg38
Supplementary_files_format_and_content: normalized bw files

growth_protocol: ChIP-seq of ER (SC-543) Santa Cruz, H3K27ac (ab4729) Abcam, GRHL1 (Novus Biologicals, NBP1-81321) and FOXA1 (ab23738) Abcam was performed. Briefly, cell samples were crosslinked with 1% formaldehyde for 10 min, and quenched by glycine to a 125nM final concentration.BAF155 and BRG1 ChIP-seq were performed as previously described by Kadoch and colleagues17. BAF155-2 (Santa Cruz, SC-9746) and BRG1-2 (Abcam, ab110641) were performed as described by Roberts and colleagues as detailed in the methods section.

extract_protocol:
The fixed cells were lysed in SDS buffer and the chromatin was sheared by Covaris sonication. The sheared chromatin was incubated with the aforementioned antibodies and protein G-Dynabeads. The samples underwent decrosslinking, RNase and proteinase K treatment.
DNA fragments were eluted using AMP Pure beads, library was prepared and samples were subjected to high-throughput sequencing using HiSeq 2000 platform (Illumina).

tag: chip-antibody

value: GRHL1 (Novus Biologicals, NBP1-81321)


title: Sample_DMSO_ET_KO_Input_2

tag: genotype


title: Sample_BT549_sg1_ARID1A_2


title: Sample_DMSO_ET_KO_FOXA1_1

value: FOXA1 (Abcam, ab23738)


title: Sample_DMSO_ET_Control_FOXA1_1


title: Sample_BT549_sg2_ARID1A_2


title: Sample_DMSO_ET_Control_GRHL1Ab1_1


title: Sample_DMSO_ET_Control_Input_1


title: Sample_DMSO_ET_Control_Input_2


title: Sample_DMSO_ET_KO_FOXA1_2


title: Sample_DMSO_CR_KO_Input_2


title: Sample_DMSO_CR_KO_Input_1


title: Sample_DMSO_CR_Control_BRG1_2


title: Sample_DMSO_CR_KO_BAF155_2

value: BAF155-2 (Santa Cruz, SC-9746)


title: Sample_DMSO_CR_Control_BAF155_2


title: Sample_DMSO_CR_KO_BRG1_2


title: Sample_DMSO_ET_Control_FOXA1_2


title: Sample_DMSO_CR_Control_Input_1


title: RNA-Seq Sample_DMSO_sg2_KO_2

source_name: Breast Cancer Cell

extract_protocol: RNA was isolated using the Qiagen RNeasy kit.


title: RNA-Seq Sample_DMSO_sg6_KO_1


title: RNA-Seq Sample_DMSO_sg2_KO_1


title: RNA-Seq Sample_DMSO_sg1_KO_2


title: RNA-Seq Sample_DMSO_sg1_KO_1


title: RNA-Seq Sample_DMSO_sg13_Control_2


title: Sample_BT549_sg2_ARID1A_1


title: Sample_DMSO_ET_KO_Input_1


title: RNA-Seq Sample_DMSO_sg12_Control_2


title: RNA-Seq Sample_DMSO_sg12_Control_1


title: ChIP-Seq Sample_DMSO_sg2_KO_Input_2

extract_protocol:
Cell samples were crosslinked with 1% formaldehyde for 10 min, and quenched by glycine to a 125nM final concentration. The fixed cells were lysed in SDS buffer and the chromatin was sheared by Covaris sonication. The sheared chromatin was incubated with the indicated antibodies and protein G-Dynabeads. The samples underwent decrosslinking, RNase and proteinase K treatment. DNA fragments were eluted using AMP Pure beads
ChIP-seq libraries were prepared using 10 ng of DNA and Illumina's TruSeq ChIP sample prep.Libraries were validated using the Agient Technologies 2100 Bioanalyzer and Qubit high sensitivity assay.


title: RNA-Seq Sample_DMSO_sg6_KO_2


title: ChIP-Seq Sample_DMSO_sg1_KO_Input_2


title: ChIP-Seq Sample_DMSO_sg2_KO_H3K27ac_2


title: ChIP-Seq Sample_DMSO_sg1_KO_Input_1


title: ChIP-Seq Sample_DMSO_sg12_Control_Input_2


title: ChIP-Seq Sample_DMSO_sg1_KO_H3K27ac_1


title: Sample_MCF7_sg1_SMARCE1_1


title: ChIP-Seq Sample_DMSO_sg12_Control_H3K27ac_1


title: ChIP-Seq Sample_DMSO_sg12_Control_H3K27ac_2


title: ChIP-Seq Sample_DMSO_sg1_KO_ER_1

value: ER


title: ChIP-Seq Sample_DMSO_sg2_KO_Input_1


title: ChIP-Seq Sample_DMSO_MCF7_Control_Input_1


title: ChIP-Seq Sample_DMSO_MCF7_KO_Input_1


title: ChIP-Seq Sample_DMSO_sg2_KO_ER_2


title: ChIP-Seq Sample_DMSO_MCF7_KO_BAF155_1


title: ChIP-Seq Sample_DMSO_sg1_KO_ER_2


title: ChIP-Seq Sample_DMSO_sg12_Control_ER_2


title: ChIP-Seq Sample_DMSO_sg2_KO_ER_1


title: ChIP-Seq Sample_DMSO_sg2_KO_H3K27ac_1


title: ChIP-Seq Sample_DMSO_MCF7_Control_BAF155_1


title: ChIP-Seq Sample_DMSO_MCF7_KO_BRG_1

value: BRG


title: ChIP-Seq Sample_DMSO_sg12_Control_ER_1


title: RNA-Seq Sample_DMSO_sg13_Control_1


title: ChIP-Seq Sample_DMSO_MCF7_Control_BRG_1


title: ATAC-Seq Sample_FULV_sg6_KO_1

data_processing:
Raw reads were trimmed using trimmomatic (v0.35, Parameters: TruSeq3-PE adapters, LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36).
Each sample was aligned to hg38 genome using bowtie2 (v2.2.6, Parameters: -X2000 –local –mm --no-mixed --no-discordant).
Duplicate reads were then removed using MarkDuplicates (v2.9.0, REMOVE_DUPLICATES=True).
In order to account for Tn5 shift, all positive strand reads in each sample were shifted by +4bps and all negative strand reads were shifted by -5bps.
Peak calling was first performed on after pooling all samples using MACS2 (v2.1.0, parameters: --nomodel --extsize 150 --shift -75 --slocal 5000 --llocal 20000 -B --keep-dup all -p 0.05) and then on individual samples (-p 0.01).
BigWig tracks were generated using MACS2 and then scaled using rtracklayer (v1.40.6).
Genome_build: hg38
Supplementary_files_format_and_content: normalized bw files

extract_protocol:
ATAC-seq was performed as described by Buenrostro et al, 2013 with the exception that 0.2% NP40 was used for cell lysis.
ATAC-seq libraries were prepared using Illumina's TruSeq ChIP sample prep.Libraries were validated using the Agient Technologies 2100 Bioanalyzer and Qubit high sensitivity assay.

treatment_protocol: MCF7 cells were treated with DMSO of Fulvestrant (100nM) for 24 hours.

tag: treatment

value: Fulvestrant


title: ATAC-Seq Sample_FULV_sg6_KO_2


title: ATAC-Seq Sample_FULV_sg2_KO_2


title: ChIP-Seq Sample_DMSO_sg1_KO_H3K27ac_2


title: ChIP-Seq Sample_DMSO_sg12_Control_Input_1


title: ATAC-Seq Sample_FULV_sg13_Control_2


title: ATAC-Seq Sample_FULV_sg1_KO_1


title: ATAC-Seq Sample_FULV_sg2_KO_1


title: ATAC-Seq Sample_FULV_sg13_Control_1


title: ATAC-Seq Sample_DMSO_sg1_KO_1

value: DMSO


title: ATAC-Seq Sample_FULV_sg1_KO_2


title: ATAC-Seq Sample_DMSO_sg1_KO_2


title: ATAC-Seq Sample_DMSO_sg12_Control_2


title: ATAC-Seq Sample_FULV_sg12_Control_1


title: ATAC-Seq Sample_DMSO_sg6_KO_1


title: ATAC-Seq Sample_FULV_sg12_Control_2


title: matrix vesicles 3

city: Hiroshima

first: Tomoko

last: Minamizaki

state: Hiroshima

address: 1-2-3, Kasumi

institute: Hiroshima University

description: miRNA in matrix vesicles

hyb_protocol: Hybridization was performed using Hyb kit and a SurePrint G3 mouse miRNA microarray rel.17 kit.

scan_protocol: miRNA profiling was analyzed using an Agilent G2539A microarray scanner with the software Scan Control (version A.8.5.1). Dye channel, Green; Scan region, Agilend HD (61x21.6mm); R/G PMT gain, 100%; Scan resolution, 3 micro m; No XDR.

data_processing:
Data was processed using Feature Extraction (version 10.10.1.1); Grit template, 035430_D_F_20121221; FE protocol, miRNA_1010_Sep10. Data was analyzed using an analysis software GeneSpring GX (version 12.5.0. Select Technology, 35230_v18.0.
Nomalization, "percentile Shift=90"; Baseline Options, "Do not perform baseline transformation"; Statistical Analysis, "Moderated t-test" "Benjamin Hochberg FDR" "p value<0.05"; Fold Change, "Cut Off =1.1"

source_name: matrix vesicles, replicate 1

label_protocol: Probe labeling using 100 ng of total RNA wss performed using a miRNA Complete Labeling.

extract_protocol: When the osteoid-like nodules formed, cultures were treated with 500 units/mL collagenase at 37 Cº for 45 min under static conditions for 15 min with shaking. Samples were then centrifuged at 20,000 x g for 20min, and wupernatants were centrifuged at 100,000 x g for 60 min. THe resultant pellets were resuspended in 100 mM mannnitol in 10 mM HEPES, followed by centrifugation at 350,000 x g for 30 min. Matrix vesicle  pellets were resuspended in PBS.

treatment_protocol: MC3T3-E1 cells were grown at 3,000 cells/cm^2 in osteogenic meium with beta-glycerophosphate.

tag: tissue

value: matrix vesicles


title: matrix vesicles 2

description: miRNA in matrix vesicles


title: ATAC-Seq Sample_DMSO_sg6_KO_2


title: ATAC-Seq Sample_DMSO_sg13_Control_1


title: matrix vesicles 1

description: miRNA in matrix vesicles


title: ATAC-Seq Sample_DMSO_sg12_Control_1


title: ATAC-Seq Sample_DMSO_sg2_KO_1


title: RNA_T24_NSD_T0N5_2

city: Lausanne

first: Maxime

last: Jan

state: Suisse

address: University of Lausanne

department: CIG

institute: University of Lausanne

description: Quantification of total RNA in mouse cortex (12:12 Light-Dark). Control sample with ad libitum sleep. (Time: 24  CTime: 0 )

data_processing:
RNA-seq data were processed using the Illumina Pipeline Software version 1.82. All RNA-seq samples passed FastQC quality thresholds (version 0.10.1) and could thus be used in subsequent analysis.
Transcript abundance was quantified by kallisto version 0.43.0 (56) using the GRCm38 reference transcriptome (mm10) and the parameters --single -l 100 -s 20 -b 100. The abundances were processed as follows using sleuth version 0.29.0: transcript abundances were merged into gene counts in transcripts per million (TPM), after which we applied a detection cutoff of 5.5 on the mean gene counts across samples in the time series. Batch effects were corrected by ComBat.Transcript abundance was quantified by kallisto version 0.43.0 (56) using the GRCm38 reference transcriptome (mm10) and the parameters --single -l 100 -s 20 -b 100. The abundances were processed as follows using sleuth version 0.29.0: transcript abundances were merged into gene counts in transcripts per million (TPM), after which we applied a detection cutoff of 5.5 on the mean gene counts across samples in the time series. Batch effects were corrected by ComBat.
ATAC-seq reads were aligned to the mouse genome (mm10) using bowtie2 in paired-end mode, with the parameters recommended for open chromatin (--very-sensitive --maxins 2000 --no-mixed --no-discordant). Duplicatesequences were removed using samtools rmdup.
ATAC-seq data files were processed before peak calling as follows. Alignment files were converted into bed files and tags were extracted using bedtools version 2.26.0. Each tag position was shifted +4 base pairs on the positive strand and - 5 base pairs on the negative strand to center tags on transposase binding events.
The peak calling was performed on pooled tags for replicates using Macs2 version 2.1.1 [--nomodel --shift -75 --extsize 150], and peaks were filtered using a 0.05 FDR cutoff for a local random Poisson distributed background noise, captured by Macs2.
Peak boundaries were merged between time points and conditions in order to build a common peak mapping reference covering all samples. Finally, peak coverage was quantified using HTSeq version 0.6.1 for each sample, using the common mapping reference. We filtered low coverage peaks using a minimum mean threshold of 10 reads per peak.
Genome_build: mm10
Supplementary_files_format_and_content: Chromatin accessibility (peak coverage) [CPM], Coordinate of ATAC peaks, Gene expression [log2 TPM]

source_name: Cerebral cortex tissue

growth_protocol: Mice were housed under standard conditions according to the Swiss Animal Protection Act, under a 12h:12h light/dark cycle, with food accessible ad libitum at all times.

extract_protocol:
Mice were anesthetized with isoflurane prior to decapitation. Cortex was rapidly dissected and flash frozen in liquid nitrogen. Frozen cortex of each individual was ground in liquid nitrogen and stored at -80°C until further use. Tissue from each mouse was distributed to the two protocols (RNAseq and ATAC-seq), such that both datasets originate from the exact same set of individuals.
Total RNA was extracted using the miRNeasy kit (Qiagen; Hilden, Germany) following the manufacturer's instructions. RNA-seq libraries were prepared using 1000 ng of total RNA and the Illumina TruSeq Stranded mRNA reagents (Illumina; San Diego, CA, USA) on a Sciclone liquid handling robot (PerkinElmer; Waltham, MA, USA) using a PerkinElmerdeveloped automated script. Libraries were sequenced on the Illumina HiSeq 2500 sequencer, producing >36 million (median 55 million) mappable single-end 100 bp reads. ATAC-seq was performed as followed, 100'000 nuclei were treated with 2.5 μl Tagment DNA enzyme (Nextera DNA Sample Preparation Kit, Illumina) in transposition buffer (10mM Tris Base, 5mM MgCl2, 10% DMSO, pH 7.6) at 37°C for 30 minutes, followed by cleanup on a Qiagen Minelute column. Fragments >1kb in size were removed using 0.6X, then 1X, volumes of AmpureXP beads (Beckman Coulter Life Sciences; Indianapolis, IN, USA). DNA fragments were subjected to 11 cycles of PCR amplification with Nextera dual index primers (Illumina) and the NEBNext High Fidelity 2X PCR Master Mix (New England Biolabs; Ipswich, MA, USA). PCR reactions were cleaned up with one volume AmpureXP beads, quantified by Qubit (ThermoFisher Scientific; Waltham, MA, USA) and quality controlled by Fragment Analyzer (Advanced Analytical Technologies; Ankeny, IA, USA). Libraries were sequenced on the Illumina HiSeq 2500 sequencer, producing >25 million (median 41 million) mappable 50 bp paired-end reads per sample after removal of duplicate and mitochondrial sequences.

treatment_protocol: Mice for tissue collection were divided into two experimental cohorts, sleep deprived (SD) and non-sleep deprived (controls, Ctr). After a one-week habituation to the experimental setting, at the age of 11-12 weeks, the SD mice were sleep-deprived by gentle handling for 6 hours starting at light onset (zeitgeber time ZT0-ZT6), and allowed to recover according to the tissue collection schedule.

tag: ztime

tag: time

tag: condition

value: NSD

tag: batch

tag: 7 days after sd

tag: strain

tag: gender

value: male


title: ATAC_T0_NSD_T0N8

description: Quantification of chromatin acessibility in mouse cortex (12:12 LD).  Control sample with ad libitum sleep. (Time: 0  CTime: 0 )


title: ATAC_T24_NSD_T0N9

description: Quantification of chromatin acessibility in mouse cortex (12:12 LD).  Control sample with ad libitum sleep. (Time: 24  CTime: 0 )


title: ATAC_T24_NSD_T0N5


title: ATAC-Seq Sample_DMSO_sg2_KO_2

tag: cell line


title: ATAC-Seq Sample_DMSO_sg13_Control_2


title: CLOCK mutant-ZT2

city: Beijing

first: Yanli

last: Wang

state: Beijing

address: State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center

description: miRNA expression in clock mutant mouse at ZT2

hyb_protocol: 875ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2565BA).

data_processing: The scanned images were analyzed using Agilent feature extraction software. Data is analyzed using Agi4x44PreProcess (Agilent Technologies).

source_name: liver, ZT2

label_protocol: Cyanine-3 (Cy3) labeled cRNA sample 4 ug  using the Low RNA Input Linear Amplication kit (Agilent, 5184-3523) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN RNeasy® Mini Kit).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: The three RNA samples at each time point were mixed and isolated using the mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556). RNA labeling, microarray hybridization and data processing were analyzed by Shanghai OE Biotech. Co., Ltd.

treatment_protocol: Clock mutant mice (Clock△19) were acquired from the Institute of Psychology, Chinese Academy of Sciences, Beijing, China. All male mice at 6-8 weeks of age used in this study were individually caged and maintained under IVC conditions with 12h light/dark cycle, lights-on at 0700hr and free access to food and water for two weeks before using. At 0900h (ZT2), 2100h (ZT14) on the first day after two weeks adaptation period, three animals of each group were sacrificed by dry ice. The liver was isolated, quickly frozen and stored in liquid nitrogen.

value: liver

tag: time point

value: CLOCK mutant


title: ATAC_T24_NSD_T0N3_2


title: ATAC_T24_NSD_T0N3


title: CLOCK mutant-ZT14

institute: State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center

description: miRNA expression in clock mutant mouse at ZT14

source_name: liver, ZT14


title: WT-ZT2

description: miRNA expression in wild type mouse at ZT2

value: WT


title: WT-ZT14

description: miRNA expression in wild type mouse at ZT14


title: ATAC_T0_NSD_T0N2


title: ATAC_T0_NSD_T0N1


title: ATAC_T30_SD_T30S4

description: Quantification of chromatin acessibility in mouse cortex (12:12 LD).  Sample taken after sleep deprivation. (Time: 30  CTime: 6 )

value: SD


title: ATAC_T78_SD_T78S2

description: Quantification of chromatin acessibility in mouse cortex (12:12 LD).  Sample taken after sleep deprivation. (Time: 78  CTime: 6 )


title: ATAC_T30_SD_T30S3


title: ATAC_T6_NSD_T6N4

description: Quantification of chromatin acessibility in mouse cortex (12:12 LD).  Control sample with ad libitum sleep. (Time: 6  CTime: 6 )


title: ATAC_T78_SD_T78S3


title: ATAC_T6_NSD_T6N2


title: ATAC_T30_SD_T30S1


title: ATAC_T72_SD_T72S4

description: Quantification of chromatin acessibility in mouse cortex (12:12 LD).  Sample taken after sleep deprivation. (Time: 72  CTime: 0 )


title: ATAC_T6_NSD_T6N3


title: ATAC_T78_SD_T78S4


title: ATAC_T66_SD_T66S2

description: Quantification of chromatin acessibility in mouse cortex (12:12 LD).  Sample taken after sleep deprivation. (Time: 66  CTime: 18 )


title: ATAC_T27_SD_T27S2

description: Quantification of chromatin acessibility in mouse cortex (12:12 Light-Dark). Sample taken after sleep deprivation. (Time: 27  CTime: 3 )


title: ATAC_T27_SD_T27S3

description: Quantification of chromatin acessibility in mouse cortex (12:12 LD).  Sample taken after sleep deprivation. (Time: 27  CTime: 3 )


title: ATAC_T27_SD_T27S5


title: ATAC_T72_SD_T72S3


title: ATAC_T3_NSD_T3N2

description: Quantification of chromatin acessibility in mouse cortex (12:12 LD).  Control sample with ad libitum sleep. (Time: 3  CTime: 3 )


title: ATAC_T3_NSD_T3N4


title: ATAC_T60_SD_T60S3

description: Quantification of chromatin acessibility in mouse cortex (12:12 LD).  Sample taken after sleep deprivation. (Time: 60  CTime: 12 )


title: ATAC_T60_SD_T60S2


title: ATAC_T72_SD_T72S2


title: ATAC_T54_SD_T54S4

description: Quantification of chromatin acessibility in mouse cortex (12:12 LD).  Sample taken after sleep deprivation. (Time: 54  CTime: 6 )


title: ATAC_T54_SD_T54S2


title: ATAC_T54_SD_T54S1


title: ATAC_T48_SD_T48S3

description: Quantification of chromatin acessibility in mouse cortex (12:12 LD).  Sample taken after sleep deprivation. (Time: 48  CTime: 0 )


title: ATAC_T48_SD_T48S4


title: ATAC_T3_NSD_T3N3


title: ATAC_T60_SD_T60S4


title: ATAC_T18_NSD_T18N8

description: Quantification of chromatin acessibility in mouse cortex (12:12 LD).  Control sample with ad libitum sleep. (Time: 18  CTime: 18 )


title: ATAC_T42_SD_T42S4

description: Quantification of chromatin acessibility in mouse cortex (12:12 LD).  Sample taken after sleep deprivation. (Time: 42  CTime: 18 )


title: ATAC_T42_SD_T42S2

description: Quantification of chromatin acessibility in mouse cortex (12:12 Light-Dark). Sample taken after sleep deprivation. (Time: 42  CTime: 18 )


title: ATAC_T12_NSD_T12N5

description: Quantification of chromatin acessibility in mouse cortex (12:12 LD).  Control sample with ad libitum sleep. (Time: 12  CTime: 12 )


title: ATAC_T18_NSD_T18N3


title: ATAC_T18_NSD_T18N2


title: ATAC_T12_NSD_T12N6


title: ATAC_T36_SD_T36S2

description: Quantification of chromatin acessibility in mouse cortex (12:12 LD).  Sample taken during sleep deprivation. (Time: 36  CTime: 12 )


title: ATAC_T18_NSD_T18N4


title: ATAC_T36_SD_T36S1


title: ATAC_T36_SD_T36S4


title: ATAC_T12_NSD_T12N2


title: ATAC_T198_SD_J76S2

description: Quantification of chromatin acessibility in mouse cortex (12:12 LD).  Sample taken after sleep deprivation. (Time: 198  CTime: 6 ) . Group sampled 7 days after sleep deprivation [SD]


title: ATAC_T48_SD_T48S1


title: ATAC_T42_SD_T42S6


title: ATAC_T198_SD_J76S1


title: ATAC_T6_NSD_J76N2

description: Quantification of chromatin acessibility in mouse cortex (12:12 LD).  Control sample with ad libitum sleep. (Time: 6  CTime: 6 ). Group sampled 7 days after sleep deprivation [Control]

value: Control


title: ATAC_T6_NSD_J76N1


title: ATAC_T192_SD_J70S3

description: Quantification of chromatin acessibility in mouse cortex (12:12 LD).  Sample taken after sleep deprivation. (Time: 192  CTime: 0 ). Group sampled 7 days after sleep deprivation [SD]


title: ATAC_T192_SD_J70S2


title: ATAC_T24_NSD_J70N2

description: Quantification of chromatin acessibility in mouse cortex (12:12 LD).  Control sample with ad libitum sleep. (Time: 24  CTime: 0 ). Group sampled 7 days after sleep deprivation [Control]


title: ATAC_T192_SD_J70S1


title: ATAC_T0_NSD_J70N1

description: Quantification of chromatin acessibility in mouse cortex (12:12 LD).  Control sample with ad libitum sleep. (Time: 0  CTime: 0 ). Group sampled 7 days after sleep deprivation [Control]


title: WP_HA-mERa_AdCre_MMECs_DMSO_repl1

city: Amsterdam

first: Lisette

last: Cornelissen

address: Plesmanlaan 121

country: Netherlands

institute: The Netherlands Cancer Institute

data_processing:
Libraries were generated with the Illumina TruSeq RNA Library Preparation kit (RS-122-2001/2, Illumina Inc.) and sequenced on a HiSeq 2500 (using 65bp reads)
Sequencing data was aligned to GRCh38 (MCF7) or GRCm38 (MMECs) using TopHat and number of reads per gene were measured with HTSeq count.
Read counts were corrected for differences in sequencing depth by using DESeqs median-of-ratios and the normalized counts were log2-transformed.
Genome_build: GRCh38 (MCF7), GRCm38 (MMECs)
Supplementary_files_format_and_content: Expression table of samples (columns) by transcript (rows) reporting normalized counts.

source_name: Primary mouse mammary epithelial cells

extract_protocol:
RNA was extracted using the AllPrep DNA/RNA universal kit (Qiagen) according to the manufacturer’s instruction with Qiagen’s QIAcube robot. Samples with a RIN>8 were considered for library preparation.
Libraries were generated with the Illumina TruSeq RNA Library Preparation kit (RS-122-2001/2, Illumina Inc.).

value: FVB

tag: cell type

value: Primary MMECs

value: AdCre transduction followed by 72hrs hormone deprivation; 6hrs DMSO


title: ATAC_T12_NSD_T12N4


title: ATAC_T12_NSD_T12N1


title: WP_HA-mERa_AdCre_MMECs_DMSO_repl2


title: WP_AdCre_MMECs_E2_repl1


title: WP_HA-hERa_AdCre_MMECs_DMSO_repl1


title: WT_MMECs_DMSO_repl1


title: WP_AdCre_MMECs_E2_repl2

value: AdCre transduction followed by 72hrs hormone deprivation; 6hrs Estradiol


title: WP_HA-mERa_AdCre_MMECs_E2_repl2


title: ATAC_T198_SD_J76S3


title: WP_HA-hERa_AdCre_MMECs_DMSO_repl2


title: WP_HA-hERa_AdCre_MMECs_E2_repl1


title: WP_AdCre_MMECs_DMSO_repl2


title: WT_MMECs_E2_repl2


title: WT_MMECs_DMSO_repl2

value: 72hrs hormone deprivation; 6hrs DMSO


title: WP_AdCre_MMECs_DMSO_repl1


title: WP_HA-hERa_AdCre_MMECs_E2_repl2


title: WT_MMECs_E2_repl1